MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Acta Crystallographica Section D' source. Sun, 21 Mar 2010 16:57:28 +0100 http://www.medworm.com/index.php?rid=3266299&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5007 In this study, the crystal structures of the human Hsp70 nucleotide-binding domain (NBD) fragment were determined in the nucleotide-free state and in complex with adenosine 5′-(β,γ-imido)triphosphate (AMPPNP). The structure of the nucleotide-free NBD fragment is similar to that of the AMPPNP-bound NBD fragment and is designated as the `closed form'. In the nucleotide-free NBD fragment the closed form is intrinsically supported through interactions between Tyr15, Lys56 and Glu268 which connect subdomains IA, IB and IIB at the centre of the protein. Interaction with the substrate-binding domain (SBD) of Hsp70 or the BAG domain of BAG1 impairs this subdomain connection and triggers the rotation of subdomain IIA around a hydrophobic helix from subdomain IA. The subdomain rotation is limit... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266299 Fri, 12 Feb 2010 16:02:26 +0100 3266299 http://www.medworm.com/index.php?rid=3266311&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5026 An MsbA deletion mutant ΔC21 that lacks the two C-terminal α-helices was expressed in Escherichia coli strain C41 and purified by metal-affinity and gel-filtration chromatography. Purified ΔC21 retained 26% of the activity of the wild-type ATPase and had a similar binding affinity to fluorescent nucleotide derivatives. Although crystals of wild-type MsbA complexed with adenosine 5′-(β,γ-imido)triphosphate could not be obtained, crystals of ΔC21 that diffracted to 4.5 Å resolution were obtained. The preliminary ΔC21 structure had the outward-facing conformation, in contrast to the previously reported E. coli MsbA structure. This result suggests that deletion of the C-terminal α-helices may play a role in facilitating the outward-facing nucleotide-bound crystal structure of Ec... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266311 Fri, 12 Feb 2010 00:00:00 +0100 3266311 http://www.medworm.com/index.php?rid=3266310&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5028 Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monom... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266310 Fri, 12 Feb 2010 00:00:00 +0100 3266310 http://www.medworm.com/index.php?rid=3266309&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5018 An approach is presented for the structure determination of membrane proteins on the basis of poorly diffracting crystals which exploits molecular replacement for heavy-atom site identification at 6–9 Å maximum resolution and improvement of the heavy-atom-derived phases by multi-crystal averaging using quasi-isomorphous data sets. The multi-crystal averaging procedure allows real-space density averaging followed by phase combination between non-isomorphous native data sets to exploit crystal-to-crystal nonisomorphism despite the crystals belonging to the same space group. This approach has been used in the structure determination of H+-ATPase and Na+,K+-ATPase using Ca2+-ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated. (S... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266309 Fri, 12 Feb 2010 00:00:00 +0100 3266309 http://www.medworm.com/index.php?rid=3266308&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5181 The structure of a 14 kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 Å wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structure, one chloride ion turned out to be essential to achieve phasing. The minimal data requirements and the relative contributions of the Cl and S atoms to phasing are discussed. This work supports the feasibility of a systematic approach for the solution of protein crystal structures by SAD based on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substit... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266308 Fri, 12 Feb 2010 00:00:00 +0100 3266308 http://www.medworm.com/index.php?rid=3266307&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5399 The signal recognition particle (SRP) is a conserved ribonucleoprotein (RNP) complex that co-translationally targets membrane and secretory proteins to membranes. The assembly of the particle depends on the proper folding of the SRP RNA, which in mammalia and archaea involves an induced-fit mechanism within helices 6 and 8 in the S domain of SRP. The two helices are juxtaposed and clamped together upon binding of the SRP19 protein to their apices. In the current assembly paradigm, archaeal SRP19 causes the asymmetric loop of helix 8 to bulge out and expose the binding platform for the key player SRP54. Based on a heterologous archaeal SRP19–human SRP RNA structure, mammalian SRP19 was thought not to be able to induce this change, thus explaining the different requirements of SRP19 for SR... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266307 Fri, 12 Feb 2010 00:00:00 +0100 3266307 http://www.medworm.com/index.php?rid=3266306&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5184 A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate Cα positions at spacings of approximately 0.6 Å along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate Cα positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266306 Fri, 12 Feb 2010 00:00:00 +0100 3266306 http://www.medworm.com/index.php?rid=3266305&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5183 A method for rapidly building β-sheets into electron-density maps is presented. β-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and Cβ atoms along the strand averaged over all repeats present in the strand. The β-strands obtained are then assembled into a single atomic model of the β-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. The β-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 Å resolution in which a third of the residues in β-sheets were built and a structu... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266305 Fri, 12 Feb 2010 00:00:00 +0100 3266305 http://www.medworm.com/index.php?rid=3266304&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5182 A method for the identification of α-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where α-helices appear as tubes of density. The positioning and direction of the α-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. An average of 63% of the α-helical residues in these proteins were built and an average of 76% of the residues built matched helical residues in the refined models of the proteins. The overall average r.m.s.d. between main-chain atoms in the modeled α-helices and the nearest atom wi... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266304 Fri, 12 Feb 2010 00:00:00 +0100 3266304 http://www.medworm.com/index.php?rid=3266303&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5033 Haemoglobin component V (Hb V) from the midge larva Propsilocerus akamusi exhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependen... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266303 Fri, 12 Feb 2010 00:00:00 +0100 3266303 http://www.medworm.com/index.php?rid=3266302&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5150 The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)2 with pentamidine is presented. The duplex was found to have a mixed structure containing Watson–Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are a... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266302 Fri, 12 Feb 2010 00:00:00 +0100 3266302 http://www.medworm.com/index.php?rid=3266301&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5021 Although Escherichia coli alanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an α-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered α-helix did not form a leucine zipper that interlocked with the same α-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice int... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266301 Fri, 12 Feb 2010 00:00:00 +0100 3266301 http://www.medworm.com/index.php?rid=3266300&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5035 The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 Å resolution and refined as a homodimer in the hexagonal space group P61 to an Rcryst of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3266300 Fri, 12 Feb 2010 00:00:00 +0100 3266300 http://www.medworm.com/index.php?rid=3235184&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0415 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235184 Mon, 01 Feb 2010 00:00:00 +0100 3235184 http://www.medworm.com/index.php?rid=3235197&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0411 Two papers by H. M. Krishna Murthy et al. are retracted. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235197 Fri, 22 Jan 2010 00:00:00 +0100 3235197 http://www.medworm.com/index.php?rid=3235196&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5186 Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235196 Fri, 22 Jan 2010 00:00:00 +0100 3235196 http://www.medworm.com/index.php?rid=3235195&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5081 The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a critical transformation that produces the first branch-point intermediate in an essential microbial amino-acid biosynthetic pathway. The first structure of an ASADH isolated from a fungal species (Candida albicans) has been determined as a complex with its pyridine nucleotide cofactor. This enzyme is a functional dimer, with a similar overall fold and domain organization to the structurally characterized bacterial ASADHs. However, there are differences in the secondary-structural elements and in cofactor binding that are likely to cause the lower catalytic efficiency of this fungal enzyme. Alterations in the dimer interface, through deletion of a helical subdomain and replacement of amino acids that participate in a hydrog... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235195 Fri, 22 Jan 2010 00:00:00 +0100 3235195 http://www.medworm.com/index.php?rid=3235194&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5130 Mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21) is the only aldo–keto reductase that catalyzes the stereospecific reduction of 3- and 17-ketosteroids to the corresponding 3(17)α-hydroxysteroids. The Y224D mutation of AKR1C21 reduced the Km value for NADP(H) by up to 80-fold and completely reversed the 17α stereospecificity of the enzyme. The crystal structure of the Y224D mutant at 2.3 Å resolution revealed that the mutation resulted in a change in the conformation of the flexible loop B, including the V-shaped groove, which is a unique feature of the active-site architecture of wild-type AKR1C21 and is formed by the side chains of Tyr224 and Trp227. Furthermore, mutations (Y224F and Q222N) of residues involved in forming the safety belt for binding of the coenzyme showed simil... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235194 Fri, 22 Jan 2010 00:00:00 +0100 3235194 http://www.medworm.com/index.php?rid=3235193&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5135 The anaphylatoxin C5a is derived from the complement component C5 during activation of the complement cascade. It is an important component in the pathogenesis of a number of inflammatory diseases. NMR structures of human and porcine C5a have been reported; these revealed a four-helix bundle stabilized by three disulfide bonds. The crystal structure of human desArg-C5a has now been determined in two crystal forms. Surprisingly, the protein crystallizes as a dimer and each monomer in the dimer has a three-helix core instead of the four-helix bundle noted in the NMR structure determinations. Furthermore, the N-terminal helices of the two monomers occupy different positions relative to the three-helix core and are completely different from the NMR structures. The physiological significance o... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235193 Fri, 22 Jan 2010 00:00:00 +0100 3235193 http://www.medworm.com/index.php?rid=3235192&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5079 The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5′-deoxy-5′-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235192 Fri, 22 Jan 2010 00:00:00 +0100 3235192 http://www.medworm.com/index.php?rid=3235191&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5185 Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades α-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98 Å resolution. The 210 kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235191 Fri, 22 Jan 2010 00:00:00 +0100 3235191 http://www.medworm.com/index.php?rid=3235190&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5020 HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling ζ subunit of the T-cell receptor (TCRζ). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCRζ fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCRζ polypeptide (Leu51–Asp93) was determined to 3.7 Å resolution (Rwork = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCRζ polypeptide (Ala63–Arg80) was determined to 2.05 Å resolution (Rwork = 17.0%), but only after the detection of nearly perf... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235190 Fri, 22 Jan 2010 00:00:00 +0100 3235190 http://www.medworm.com/index.php?rid=3235189&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5080 Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides to the corresponding free bases and ribose 1-phosphate. The crystal structure of grouper iridovirus PNP (givPNP), corresponding to the first PNP gene to be found in a virus, was determined at 2.4 Å resolution. The crystals belonged to space group R3, with unit-cell parameters a = 193.0, c = 105.6 Å, and contained four protomers per asymmetric unit. The overall structure of givPNP shows high similarity to mammalian PNPs, having an α/β structure with a nine-stranded mixed β-barrel flanked by a total of nine α-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively. The geometrical arrangement and hydroge... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235189 Fri, 22 Jan 2010 00:00:00 +0100 3235189 http://www.medworm.com/index.php?rid=3235188&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5032 The MST family is a subclass of mammalian serine/threonine kinases that are related to the yeast sterile-20 protein and are implicated in regulating cell growth and transformation. The MST3 protein contains a 300-residue catalytic domain and a 130-residue regulatory domain, which can be cleaved by caspase and activated by autophosphorylation, promoting apoptosis. Here, five crystal structures of the catalytic domain of MST3 are presented, including a complex with ADP and manganese, a unique cofactor preferred by the enzyme, and a complex with adenine. Similar to other protein kinases, the catalytic domain of MST3 folds into two lobes: the smaller N lobe forms the nucleotide-binding site and the larger C lobe recognizes the polypeptide substrate. The bound ADP and Mn2+ ions are covered by ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235188 Fri, 22 Jan 2010 00:00:00 +0100 3235188 http://www.medworm.com/index.php?rid=3235187&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5178 Important steps in the processing of rotation data are described that are common to most software packages. These programs differ in the details and in the methods implemented to carry out the tasks. Here, the working principles underlying the data-reduction package XDS are explained, including the new features of automatic determination of spot size and reflecting range, recognition and assignment of crystal symmetry and a highly efficient algorithm for the determination of correction/scaling factors. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235187 Fri, 22 Jan 2010 00:00:00 +0100 3235187 http://www.medworm.com/index.php?rid=3235186&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5179 The usage and control of recent modifications of the program package XDS for the processing of rotation images are described in the context of previous versions. New features include automatic determination of spot size and reflecting range and recognition and assignment of crystal symmetry. Moreover, the limitations of earlier package versions on the number of correction/scaling factors and the representation of pixel contents have been removed. Large program parts have been restructured for parallel processing so that the quality and completeness of collected data can be assessed soon after measurement. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235186 Fri, 22 Jan 2010 00:00:00 +0100 3235186 http://www.medworm.com/index.php?rid=3235185&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5133 Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an αβα-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have importan... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3235185 Fri, 22 Jan 2010 00:00:00 +0100 3235185 http://www.medworm.com/index.php?rid=3110583&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0408 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110583 Tue, 22 Dec 2009 15:50:32 +0100 3110583 http://www.medworm.com/index.php?rid=3110596&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0397 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110596 Mon, 21 Dec 2009 00:00:00 +0100 3110596 http://www.medworm.com/index.php?rid=3110595&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5061 In this report, a set of algorithms is presented to characterize on-axis slow-scan large-area CCD-based TEM detectors. These tools have been added to a publicly available image-processing toolbox for MATLAB. Three in-house CCD cameras were carefully characterized, yielding, among others, statistics for hot and bad pixels, the modulation transfer function, the conversion factor, the effective gain and the detective quantum efficiency. These statistics will aid data-collection strategy programs and provide prior information for quantitative imaging. The relative performance of the characterized detectors is discussed and a comparison is made with similar detectors that are used in the field of X-ray crystallography. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110595 Mon, 21 Dec 2009 00:00:00 +0100 3110595 http://www.medworm.com/index.php?rid=3110594&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5032 Two crystal modifications of a collagen model peptide, (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 [where Hyp is (4R,2S)-l-hydroxyproline], showed very similar unit-cell parameters and belonged to the same space group P21. Both crystals exhibited pseudo-merohedral twinning. The main difference was in their molecular-packing arrangements. One modification showed pseudo-hexagonal packing, while the other showed pseudo-tetragonal packing. Despite their different packing arrangements, no significant differences were observed in the hydration states of these modifications. The peptide in the pseudo-tetragonal crystal showed a cyclic fluctuation of helical twists with a period of 20 Å, while that in the pseudo-hexagonal crystal did not. In these modifications, the puckering conformations of fou... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110594 Mon, 21 Dec 2009 00:00:00 +0100 3110594 http://www.medworm.com/index.php?rid=3110593&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5001 Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the complex of human MK2 (residues 41–364) with the potent MK2 inhibitor TEI-I01800 (pKi = 6.9) was determined at 2.9 Å resolution. The MK2 structure in the MK2–TEI-I01800 complex is composed of two domains, as observed for other Ser/Thr kinases; however, the Gly-rich loop in the N-terminal domain forms an α-helix structure and not a β-sheet. TEI-I01800 binds to the ATP-binding site as well as near the substrate-binding site of MK2. Both TEI-I01800 molecules have a nonplanar conformation that differs from those of other MK2 inhibitors deposit... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110593 Mon, 21 Dec 2009 00:00:00 +0100 3110593 http://www.medworm.com/index.php?rid=3110592&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5132 Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110592 Mon, 21 Dec 2009 00:00:00 +0100 3110592 http://www.medworm.com/index.php?rid=3110591&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5019 Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the l-lysine biosynthetic pathway. DHDPR reduces the α,β-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This con... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110591 Mon, 21 Dec 2009 00:00:00 +0100 3110591 http://www.medworm.com/index.php?rid=3110590&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5010 Uridine nucleoside phosphorylase is an important drug target for the development of anti-infective and antitumour agents. The X-ray crystal structure of Salmonella typhimurium uridine nucleoside phosphorylase (StUPh) complexed with its inhibitor 2,2′-anhydrouridine, phosphate and potassium ions has been solved and refined at 1.86 Å resolution (Rcryst = 17.6%, Rfree = 20.6%). The complex of human uridine phosphorylase I (HUPhI) with 2,2′-anhydrouridine was modelled using a computational approach. The model allowed the identification of atomic groups in 2,2′-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110590 Mon, 21 Dec 2009 00:00:00 +0100 3110590 http://www.medworm.com/index.php?rid=3110589&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5306 The second virial coefficient, or B value, is a measurement of how well a protein interacts with itself in solution. These interactions can lead to protein crystallization or precipitation, depending on their strength, with a narrow range of B values (the `crystallization slot') being known to promote crystallization. A convenient method of determining the B value is by self-interaction chromatography. This paper describes how the light-harvesting complex 1–reaction centre core complex from Allochromatium vinosum yielded single straight-edged crystals after iterative cycles of self-interaction chromatography and crystallization. This process allowed the rapid screening of small molecules and detergents as crystallization additives. Here, a description is given of how self-interaction chr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110589 Mon, 21 Dec 2009 00:00:00 +0100 3110589 http://www.medworm.com/index.php?rid=3110588&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmn5001 Family 3 carbohydrate-binding modules (CBM3s) are associated with both cellulosomal scaffoldins and family 9 glycoside hydrolases (GH9s), which are multi-modular enzymes that act on cellulosic substrates. CBM3s bind cellulose. X-ray crystal structures of these modules have established an accepted cellulose-binding mechanism based on stacking interactions between the sugar rings of cellulose and a planar array of aromatic residues located on the CBM3 surface. These planar-strip residues are generally highly conserved, although some CBM3 sequences lack one or more of these residues. In particular, CBM3b′ from Clostridium thermocellum Cel9V exhibits such sequence changes and fails to bind cellulosic substrates. A crystallographic investigation of CBM3b′ has been initiated in order to un... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110588 Mon, 21 Dec 2009 00:00:00 +0100 3110588 http://www.medworm.com/index.php?rid=3110587&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5018 Twinning is one of the most common crystal-growth defects in protein crystallography. There are neither efficient rational approaches for the growth of nontwinned protein crystals nor are there examples of systematic studies of the dependence of the twinning-ratio distribution on crystallization conditions. The description of the twinning phenomenon has been covered even less for membrane-protein crystals and is non-existent for crystals grown using lipidic phases (in meso). In the present work, possibilities for overcoming merohedral twinning are investigated for crystals of the membrane protein bacteriorhodopsin (bR) grown in meso. It is shown that traditional crystallization additives are not effective in the case of the in meso crystallization of bR. The twinning ratio was determined f... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110587 Mon, 21 Dec 2009 00:00:00 +0100 3110587 http://www.medworm.com/index.php?rid=3110586&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5175 MOLREP is an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and data preparation. Since the first publication describing the program, MOLREP has acquired a variety of features that include weighting of the X-ray data and search models, multi-copy search, fitting the model into electron density, structural superposition of two models and rigid-body refinement. The program can run in a fully automatic mode using optimized parameters calculated from the input data. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110586 Mon, 21 Dec 2009 00:00:00 +0100 3110586 http://www.medworm.com/index.php?rid=3110585&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5180 MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Adva... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110585 Mon, 21 Dec 2009 00:00:00 +0100 3110585 http://www.medworm.com/index.php?rid=3110584&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgm5005 Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a `pink' beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3110584 Mon, 21 Dec 2009 00:00:00 +0100 3110584 http://www.medworm.com/index.php?rid=3003159&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgm5010 Dehydration of protein crystals is rarely used, despite being a post-crystallization method that is useful for the improvement of crystal diffraction properties, as it is difficult to reproduce and monitor. A novel device for hydration control of macromolecular crystals in a standard data-collection environment has been developed. The device delivers an air stream of precise relative humidity that can be used to alter the amount of water in macromolecular crystals. The device can be rapidly installed and is fully compatible with most standard synchrotron X-ray beamlines. Samples are mounted in cryoloops and the progress of dehydration can be monitored both optically and by the acquisition of diffraction images. Once the optimal hydration level has been obtained, cryocooling is easy to achi... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003159 Wed, 18 Nov 2009 16:10:23 +0100 3003159 http://www.medworm.com/index.php?rid=3003171&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5137 Some of the current trends in the structure of evolutionary biology are reviewed using as a framework the book of the same title by S. J. Gould (1941–2002). The revised concepts and interpretations of the structure–function relationship in evolutionary biology are discussed in relation to the past achievements and future developments in structural biology. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003171 Tue, 17 Nov 2009 00:00:00 +0100 3003171 http://www.medworm.com/index.php?rid=3003170&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5174 Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third o... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003170 Tue, 17 Nov 2009 00:00:00 +0100 3003170 http://www.medworm.com/index.php?rid=3003169&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5029 The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without divalent cations were solved at 2.17 and 2.00 Å resolution, respectively. HindIII forms a dimer. The structures showed that HindIII belongs to the EcoRI-like (α-class) subfamily of type II restriction endonucleases. The cognate DNA-complex structures revealed the specific DNA-recognition mechanism of HindIII by which it recognizes the palindromic sequence A/AGCTT. In the Mg2+ ion-soaked structure the DNA was cleaved and two ions were bound at each active site, corresponding to the two-metal-ion mechanism. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003169 Tue, 17 Nov 2009 00:00:00 +0100 3003169 http://www.medworm.com/index.php?rid=3003168&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5173 NAD+-dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD+ to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95 Å resolution, respectively. MorFDH is similar to the previously studied FDH from the bacterium Pseudomonas sp. 101 in overall structure, cofactor-binding mode and active-site architecture, but differs in that the eight-residue-longer C-terminal fragment is visible in the electron-density maps of MorFDH. MorFDH also differs in the organization of the dimer interface. The holo MorFDH structure supports the earlier hypothesis that the catalytic residue His332 can form a hydrogen bond to both the substra... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003168 Tue, 17 Nov 2009 00:00:00 +0100 3003168 http://www.medworm.com/index.php?rid=3003167&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5078 Glycoside hydrolase family 13 (GH-13) mainly contains starch-degrading or starch-modifying enzymes. Sucrose hydrolases utilize sucrose instead of amylose as the primary glucosyl donor. Here, the catalytic properties and X-ray structure of sucrose hydrolase from Xanthomonas campestris pv. campestris are reported. Sucrose hydrolysis catalyzed by the enzyme follows Michaelis–Menten kinetics, with a Km of 60.7 mM and a kcat of 21.7 s−1. The structure of the enzyme was solved at a resolution of 1.9 Å in the resting state with an empty active site. This represents the first apo structure from subfamily 4 of GH-13. Comparisons with structures of the highly similar sucrose hydrolase from X. axonopodis pv. glycines most notably showed that residues Arg516 and Asp138, which form a salt br... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003167 Tue, 17 Nov 2009 00:00:00 +0100 3003167 http://www.medworm.com/index.php?rid=3003166&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5155 CBP and its paralog p300 are histone acetyl transferases that regulate gene expression by interacting with multiple transcription factors via specialized domains. The structure of a segment of human p300 protein (residues 1723–1836) corresponding to the extended zinc-binding Taz2 domain has been investigated. The crystal structure was solved by the SAD approach utilizing the anomalous diffraction signal of the bound Zn ions. The structure comprises an atypical helical bundle stabilized by three Zn ions and closely resembles the solution structures determined previously for shorter peptides. Residues 1813–1834 from the current construct form a helical extension of the C-terminal helix and make extensive crystal-contact interactions with the peptide-binding site of Taz2, providing add... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003166 Tue, 17 Nov 2009 00:00:00 +0100 3003166 http://www.medworm.com/index.php?rid=3003165&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5170 The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2 Å resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9 Å resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003165 Tue, 17 Nov 2009 00:00:00 +0100 3003165 http://www.medworm.com/index.php?rid=3003164&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5009 Predictions of the possible model parameterization and of the values of model characteristics such as R factors are important for macromolecular refinement and validation protocols. One of the key parameters defining these and other values is the resolution of the experimentally measured diffraction data. The higher the resolution, the larger the number of diffraction data Nref, the larger its ratio to the number Nat of non-H atoms, the more parameters per atom can be used for modelling and the more precise and detailed a model can be obtained. The ratio Nref/Nat was calculated for models deposited in the Protein Data Bank as a function of the resolution at which the structures were reported. The most frequent values for this distribution depend essentially linearly on resolution when the... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003164 Tue, 17 Nov 2009 00:00:00 +0100 3003164 http://www.medworm.com/index.php?rid=3003163&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5305 A systematic analysis was undertaken to seek correlations between the integrity, purity and activity of 50S ribosomal subunit preparations from Deinococcus radiodurans and their ability to crystallize. Conditions of fermentation, purification and crystallization were varied in a search for crystals that could reliably supply an industrial X-ray crystallography program for the structure-based design of ribosomal antibiotics. A robust protocol was obtained to routinely obtain crystals that gave diffraction patterns extending to 2.9 Å resolution and that were large enough to yield a complete data set from a single crystal. To our knowledge, this is the most systematic study of this challenging area so far undertaken. Ribosome crystallization is a complex multi-factorial problem and althoug... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003163 Tue, 17 Nov 2009 00:00:00 +0100 3003163 http://www.medworm.com/index.php?rid=3003162&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5030 Adhesion/invasion of pathogenic bacteria is a critical step in infection and is mediated by surface-exposed proteins termed adhesins. The crystal structure of recombinant Lmb, a laminin-binding adhesin from Streptococcus agalactiae, has been determined at 2.5 Å resolution. Based on sequence and structural homology, Lmb was placed into the cluster 9 family of the ABC (ATP-binding cassette) transport system. The structural organization of Lmb closely resembles that of ABC-type solute-binding proteins (SBPs), in which two structurally related globular domains interact with each other to form a metal-binding cavity at the interface. The bound zinc in Lmb is tetrahedrally coordinated by three histidines and a glutamate from both domains. A comparison of Lmb with other metal transporters re... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003162 Tue, 17 Nov 2009 00:00:00 +0100 3003162 http://www.medworm.com/index.php?rid=3003161&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5029 Bacterial l-asparaginases have been used in the treatment of childhood acute lymphoblastic leukaemia for over 30 years. Their therapeutic effect is based on their ability to catalyze the conversion of l-asparagine, an essential amino acid in certain tumours, to l-aspartic acid and ammonia. Two l-asparaginases, one from Escherichia coli and the other from Erwinia chrysanthemi, have been widely employed in clinical practice as anti-leukaemia drugs. However, l-asparaginases are also able to cause severe side effects owing to their intrinsic glutaminase activity. Helicobacter pylori l-asparaginase (HpA) has been reported to have negligible glutaminase activity. To gain insight into the properties of HpA, its crystal structure in the presence of l-aspartate was determined to 1.4 Å resolut... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003161 Tue, 17 Nov 2009 00:00:00 +0100 3003161 http://www.medworm.com/index.php?rid=3003160&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5379 α-Spectrin SH3-domain (Spc-SH3) crystallization is characterized by very fast growth of the crystals in the presence of ammonium sulfate as a precipitant agent. The origin of this behaviour can be attributed to the presence of a proline residue that participates in a crystal contact mimicking the binding of proline-rich sequences to SH3 domains. This residue, Pro20, is located in the RT loop and is the main contact in one of the interfaces present in the orthorhombic Spc-SH3 crystal structures. In order to understand the molecular interactions that are responsible for the very fast crystal growth of the wild-type (WT) Spc-SH3 crystals, the crystal structure of a triple mutant in which the residues Ser19-Pro20-Arg21 in the RT loop have been replaced by Gly19-Asp20-Ser21 (GDS Spc-SH3 mutant... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=3003160 Tue, 17 Nov 2009 00:00:00 +0100 3003160 http://www.medworm.com/index.php?rid=2919473&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5103 This paper is concerned with the effect of protein–precipitant interfaces and externally applied shear on the nucleation and growth kinetics of hen egg-white lysozyme crystals. The early stages of microbatch crystallization of lysozyme were explored using both optical and confocal fluorescence microscopy imaging. Initially, an antisolvent (precipitant) was added to a protein drop and the optical development of the protein–precipitant interface was followed with time. In the presence of the water-soluble polymer poly(ethylene glycol) (PEG) a sharp interface was observed to form immediately within the drop, giving an initial clear separation between the lighter protein solution and the heavier precipitant. This interface subsequently became unstable and quickly developed within a few sec... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919473 Fri, 23 Oct 2009 15:11:51 +0100 2919473 http://www.medworm.com/index.php?rid=2919483&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5030 Crystallization of phytochromes and other photochromic proteins is hampered by the conformational changes that they undergo on exposure to light. As a canonical phytochrome, cyanobacterial Cph1 switches between two stable states upon absorption of red/far-red light. Consequently, it is mandatory to work in darkness from protein purification to crystal cryoprotection in order to ensure complete occupancy of one state or the other. With the simple and inexpensive methods that have been developed, phytochromes and other photochromic molecules can effectively be handled and crystallized, as has been demonstrated by the solution of the three-dimensional structure of the Cph1 sensory module. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919483 Wed, 21 Oct 2009 23:00:00 +0100 2919483 http://www.medworm.com/index.php?rid=2919482&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5134 Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall kcat. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919482 Wed, 21 Oct 2009 23:00:00 +0100 2919482 http://www.medworm.com/index.php?rid=2919481&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5375 Filamin A (FLNa) is a large dimeric protein that binds to actin filaments via its actin-binding domain (ABD). The crystal structure of this domain was solved at 3.2 Å resolution. The domain adopts a closed conformation typical of other ABDs, but also forms a dimer both in crystallization conditions and in solution. The structure shows the localization of the residues mutated in patients with periventricular nodular heterotopia or otopalatodigital syndrome. Structural analysis predicts that mutations in both types of disorder may affect actin binding. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919481 Wed, 21 Oct 2009 23:00:00 +0100 2919481 http://www.medworm.com/index.php?rid=2919480&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5104 A modified SAD (single-wavelength anomalous diffraction) phasing algorithm has been introduced in the latest version of the program OASIS. In addition to direct-method phases and figures of merit, Hendrickson–Lattman coefficients that correspond to the original unresolved bimodal phase distributions are also output and used in subsequent phase-improvement procedures in combination with the improved phases. This provides the possibility of rebreaking the SAD phase ambiguity using the ever-improving phases resulting from the phase-improvement process. Tests using experimental SAD data from six known proteins showed that in all cases the new treatment produced significant improved results. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919480 Wed, 21 Oct 2009 23:00:00 +0100 2919480 http://www.medworm.com/index.php?rid=2919479&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5025 Dau c 1 is a major allergen of carrot (Daucus carota) which displays IgE cross-reactivity with the homologous major birch-pollen allergen Bet v 1. The crystal structure of Dau c 1 has been determined to a resolution of 2.7 Å, revealing tight dimers. The structure of Dau c 1 is similar to those of the major allergens from celery, Api g 1, and birch pollen, Bet v 1. Electron density has been observed in the hydrophobic cavity of each monomer and has been modelled with polyethylene glycol oligomers of varying length. Comparison of the surface topology and physicochemical properties of Dau c 1 and Bet v 1 revealed that they may have some, but not all, epitopes in common. This is in agreement with the observation that the majority of carrot-allergic patients h... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919479 Wed, 21 Oct 2009 23:00:00 +0100 2919479 http://www.medworm.com/index.php?rid=2919478&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5176 Lignin biodegradation, a key step in carbon recycling in land ecosystems, is carried out by white-rot fungi through an H2O2-dependent process defined as enzymatic combustion. Pleurotus eryngii is a selective lignin-degrading fungus that produces H2O2 during redox cycling of p-anisylic compounds involving the secreted flavoenzyme aryl-alcohol oxidase (AAO). Here, the 2.4 Å resolution X-ray crystal structure of this oxidoreductase, which catalyzes dehydrogenation reactions on various primary polyunsaturated alcohols, yielding the corresponding aldehydes, is reported. The AAO crystal structure was solved by single-wavelength anomalous diffraction of a selenomethionine derivative obtained by Escherichia coli expression and in vitro folding. This monomeric enzyme is composed of two domains,... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919478 Wed, 21 Oct 2009 23:00:00 +0100 2919478 http://www.medworm.com/index.php?rid=2919477&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5138 Drug development against Leishmania donovani, the pathogen that causes visceral leishmaniasis in humans, is currently an active area of research given the widespread prevalence of the disease and the emergence of resistant strains. The immunosuppressive drug cyclosporin is known to have antiparasitic activity against a variety of pathogens. The receptor for cyclosporin is the protein cyclophilin, which is a ubiquitous peptidylprolyl isomerase. The crystal structure of cyclophilin from L. donovani complexed with cyclosporin has been solved at 2.6 Å resolution. The thermodynamic parameters of the interaction have been determined using spectroscopic and calorimetric techniques. A detailed effort has been made to predict the thermodynamic parameters of binding from computations based on th... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919477 Wed, 21 Oct 2009 23:00:00 +0100 2919477 http://www.medworm.com/index.php?rid=2919476&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5378 The structure of the nucleotide-binding domain of the Mg-ATPase MgtA from Escherichia coli has been solved and refined to 1.6 Å resolution. The structure is made up of a six-stranded β-sheet and a bundle of three α-helices, with the nucleotide-binding site sandwiched in between. The MgtA nucleotide-binding domain is shorter and more compact compared with that of the related Ca-ATPase and lacks one of the β-strands at the edge of the β-sheet. The ATP-binding pocket is surrounded by three sequence and structural motifs known from other P-type ATPases and a fourth unique motif that is found only in Mg-ATPases. This motif consists of a short polypeptide stretch running very close to the ATP-binding site, while in Ca-ATPase the binding site is more open, with the corresponding polypepti... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919476 Wed, 21 Oct 2009 23:00:00 +0100 2919476 http://www.medworm.com/index.php?rid=2919475&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5017 The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008), Nature (London), 454, 177–18... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919475 Wed, 21 Oct 2009 23:00:00 +0100 2919475 http://www.medworm.com/index.php?rid=2919474&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5165 Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent `noise', showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2919474 Wed, 21 Oct 2009 23:00:00 +0100 2919474 http://www.medworm.com/index.php?rid=2799854&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5167 Dual-specificity phosphatases (DUSPs) are enzymes that participate in the regulation of biological processes such as cell growth, differentiation, transcription and metabolism. A number of DUSPs are able to dephosphorylate phosphorylated serine, threonine and tyrosine residues on mitogen-activated protein kinases (MAPKs) and thus are also classified as MAPK phosphatases (MKPs). As an increasing number of DUSPs are being identified and characterized, there is a growing need to understand their biological activities at the molecular level. There is also significant interest in identifying DUSPs that could be potential targets for drugs that modulate MAPK-dependent signaling and immune responses, which have been implicated in a variety of maladies including cancer, infectious diseases and inf... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799854 Wed, 16 Sep 2009 17:47:03 +0100 2799854 http://www.medworm.com/index.php?rid=2799865&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5076 Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P21 crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-barrel and (iii) in ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799865 Tue, 15 Sep 2009 23:00:00 +0100 2799865 http://www.medworm.com/index.php?rid=2799864&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5148 In this study, a new algorithm for the automatic modelling of discrete heterogeneity is presented. At high resolution, the authors' single multi-conformer model, with correlated structural features to represent heterogeneity, shows improved agreement with the diffraction data compared with a single-conformer model. The model appears to be representative of the set of structures present in the crystal. In contrast, below 2 Å resolution representing ambiguous electron density by correlated multi-conformers in a single model does not yield better agreement with the experimental data. Consistent with previous studies, this suggests that variability in multi-conformer models at lower resolution levels reflects uncertainty more than coordinated motion. (Source: Acta Crystallographica Section ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799864 Tue, 15 Sep 2009 23:00:00 +0100 2799864 http://www.medworm.com/index.php?rid=2799863&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5077 d-Alanine-d-alanine ligase (Ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. The enzyme catalyzes the condensation of two d-Ala molecules using ATP to produce d-Ala-d-Ala, which is the terminal peptide of a peptidoglycan monomer. The structures of five forms of the enzyme from Thermus thermophilus HB8 (TtDdl) were determined: unliganded TtDdl (2.3 Å resolution), TtDdl–adenylyl imidodiphosphate (2.6 Å), TtDdl–ADP (2.2 Å), TtDdl–ADP–d-Ala (1.9 Å) and TtDdl–ATP–d-Ala-d-Ala (2.3 Å). The central domain rotates as a rigid body towards the active site in a cumulative manner in concert with the local conformational change of three flexible loops depending upon substrate or product binding, resulting in an overal... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799863 Tue, 15 Sep 2009 23:00:00 +0100 2799863 http://www.medworm.com/index.php?rid=2799862&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5131 A combination of molecular replacement and single-wavelength anomalous diffraction phasing has been incorporated into the automated structure-determination platform Auto-Rickshaw. The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building. The improvement over the standard SAD or MR approaches is illustrated by ten test cases taken from the JCSG diffraction data-set database. Poor MR or SAD phases with phase errors larger than 70° can be improved using the described procedure and a large fraction of the model can be determined in a purely automatic manner from X-ray data extending to better than 2.6 Å resolution. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799862 Tue, 15 Sep 2009 23:00:00 +0100 2799862 http://www.medworm.com/index.php?rid=2799861&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5108 The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (Rfree = 25%). PCNA from H. volcanii was found to be homotri... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799861 Tue, 15 Sep 2009 23:00:00 +0100 2799861 http://www.medworm.com/index.php?rid=2799860&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5105 The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses simple and fast quantum-chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow the attainment of a number of diverse goals including geometry optimization and generation of restraints. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799860 Tue, 15 Sep 2009 23:00:00 +0100 2799860 http://www.medworm.com/index.php?rid=2799859&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5288 When starting a protein-crystallization project, scientists are faced with several unknowns. Amongst them are these questions: (i) is the purity of the starting material sufficient? and (ii) which type of crystallization experiment is the most promising to conduct? The difficulty in purifying active membrane-protein samples for crystallization trials and the high costs associated with producing such samples require an extremely pragmatic approach. Additionally, practical guidelines are needed to increase the efficiency of membrane-protein crystallization. In order to address these conundrums, the effects of commonly encountered impurities on various membrane-protein crystallization regimes have been investigated and it was found that the lipidic cubic phase (LCP) based crystallization meth... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799859 Tue, 15 Sep 2009 23:00:00 +0100 2799859 http://www.medworm.com/index.php?rid=2799858&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5102 A likelihood function based on the multivariate probability distribution of all observed structure-factor amplitudes from a single isomorphous replacement with anomalous scattering experiment has been derived and implemented for use in substructure refinement and phasing as well as macromolecular model refinement. Efficient calculation of a multidimensional integration required for function evaluation has been achieved by approximations based on the function's properties. The use of the function in both phasing and protein model building with iterative refinement was essential for successful automated model building in the test cases presented. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799858 Tue, 15 Sep 2009 23:00:00 +0100 2799858 http://www.medworm.com/index.php?rid=2799857&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5122 Neutron diffraction data for T6 porcine insulin were collected to 2.1 Å resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structure was refined to a residual of 0.179. The hydrogen-bonding network of the central core of the hexamer was observed and the charge balance between positively charged Zn ions and their surrounding structure was interpreted by considering the protonation and/or deprotonation states and interactions of HisB10, water and GluB13. The observed double conformation of GluB13 was essential to interpreting the charge balance and could be compared with the structure of a dried crystal of T6 human insulin at 100 K. Differences in the dynamic behaviour o... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799857 Tue, 15 Sep 2009 23:00:00 +0100 2799857 http://www.medworm.com/index.php?rid=2799856&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5024 In this study, high-resolution structures of all-α proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N–N, N–C, C–C, N–MID and C–MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their pre... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799856 Tue, 15 Sep 2009 23:00:00 +0100 2799856 http://www.medworm.com/index.php?rid=2799855&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5075 The Tbd_0210 gene of the chemolithotrophic bacterium Thiobacillus denitrificans is annotated to encode a 60.5 kDa bifunctional enzyme with ATP sulfurylase and APS kinase activity. This putative bifunctional enzyme was cloned, expressed and structurally characterized. The 2.95 Å resolution X-ray crystal structure reported here revealed a hexameric assembly with D3 symmetry. Each subunit contains a large N-terminal sulfurylase-like domain and a C-terminal APS kinase domain reminiscent of the two-domain fungal ATP sulfurylases of Penicillium chrysogenum and Saccharomyces cerevisiae, which also exhibit a hexameric assembly. However, the T. denitrificans enzyme exhibits numerous structural and sequence differences in the N-terminal domain that render it inactive with respect to ATP sulfury... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2799855 Tue, 15 Sep 2009 23:00:00 +0100 2799855 http://www.medworm.com/index.php?rid=2698864&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5007 The density-modification procedures incorporated in ACORN, available in the CCP4 package, have proved to be very successful in solving and refining high-resolution crystal structures from very poor starting sets. These can be calculated from a correctly positioned initial fragment containing between 1 and 8% of the scattering power of the total structure. Improvements of ACORN, reported here and incorporated in the program ACORN2, have lowered the size of the fragment required and examples are given of structures solved with only 0.25% of the scattering power in the fragment, which may be a single atom. Applications of ACORN2 to structures with space group P1 have shown the remarkable property that when the starting point is a pair of equal atoms, or even a single atom placed at the origin... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698864 Fri, 14 Aug 2009 11:33:57 +0100 2698864 http://www.medworm.com/index.php?rid=2698876&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpf0071 (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698876 Thu, 13 Aug 2009 23:00:00 +0100 2698876 http://www.medworm.com/index.php?rid=2698875&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5169 A response is published to the comment by Okuyama et al. [(2009) Acta Cryst. D65, 1007–1008] on Microfibrillar structure of type I collagen in situ. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698875 Thu, 13 Aug 2009 23:00:00 +0100 2698875 http://www.medworm.com/index.php?rid=2698874&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5161 A comment is published on the article Microfibrillar structure of type I collagen in situ by Orgel et al. [(2006), Proc. Natl Acad. Sci. USA, 103, 9001–9005]. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698874 Thu, 13 Aug 2009 23:00:00 +0100 2698874 http://www.medworm.com/index.php?rid=2698873&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgm5008 Analysis of a series of diffraction data sets measured from four native as well as four nicotinic acid-soaked crystals of trypsin at 100 K shows a high variability in radiation-sensitivity among individual crystals for both nicotinic acid-soaked and native crystals. The level of radiation-sensitivity and the extent of its variability is statistically indistinguishable between the two conditions. This suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation. This is in contrast to previous results [Kauffmann et al. (2006), Structure, 14, 1099–1105] where only one crystal specimen was used for each condition (native and nicotinic acid-soaked). (Source: Acta Crystallographica S... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698873 Thu, 13 Aug 2009 23:00:00 +0100 2698873 http://www.medworm.com/index.php?rid=2698872&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5008 Crystallization trials can be designed as a systematic gradient of the concentration of key reagents and/or pH centered on the original conditions. While the concept of the grid screen is simple, its implementation is tedious and difficult by hand. A procedure has been developed for preparing crystallization grid screens that is both efficient and achieves high accuracy because it relies on a limited number of solutions that are carefully prepared by hand. The `four-corners' approach to designing grid screens uses the minimum and maximum concentrations of the components being varied in the grid screen as the sole stock solutions. For an N-dimensional grid only 2N corner solutions require detailed preparation, making the screens efficient. Furthermore, by keeping the concentrations as tight... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698872 Thu, 13 Aug 2009 23:00:00 +0100 2698872 http://www.medworm.com/index.php?rid=2698871&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5134 Together with leucoanthocyanidin reductase, anthocyanidin reductase (ANR) is one of the two enzymes of the flavonoid-biosynthesis pathway that produces the flavan-3-ol monomers required for the formation of proanthocyanidins or condensed tannins. It has been shown to catalyse the double reduction of anthocyanidins to form 2R,3R-flavan-3-ols, which can be further transformed to the 2S,3R isomers by non-enzymatic epimerization. ANR from grape (Vitis vinifera) was expressed in Escherichia coli and purified. Unexpectedly, RP-HPLC, LC-MS and NMR experiments clearly established that the enzyme produces a 50:50 mixture of 2,3-cis and 2,3-trans flavan-3-ols which have been identified by chiral chromatography to be 2S,3S- and 2S,3R-flavan-3-ols, i.e. the naturally rare (+)-epicatechin and (−)-cat... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698871 Thu, 13 Aug 2009 23:00:00 +0100 2698871 http://www.medworm.com/index.php?rid=2698870&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5107 Lattice-translocation or crystal order–disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two la... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698870 Thu, 13 Aug 2009 23:00:00 +0100 2698870 http://www.medworm.com/index.php?rid=2698869&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5168 The crystal structure of the single-stranded DNA-binding protein (SSB) from Streptomyces coelicolor, a filamentous soil bacterium with a complex life cycle and a linear chromosome, has been solved and refined at 2.1 Å resolution. The three-dimensional structure shows a common conserved central OB-fold that is found in all structurally determined SSB proteins. However, it shows variations in quaternary structure that have previously only been found in mycobacterial SSBs. The strand involved in the clamp mechanism characteristic of this type of quaternary structure leads to higher stability of the homotetramer. To the best of our knowledge, this is the first X-ray structure of an SSB protein from a member of the genus Streptomyces and it was predicted to be the most stable of the structur... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698869 Thu, 13 Aug 2009 23:00:00 +0100 2698869 http://www.medworm.com/index.php?rid=2698868&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5016 In this report, LTD theory is extended and a new general method for determining defect fractions is developed based on the heights of the non-origin peaks observed in native Patterson maps. The application of this method to crystals of lentiviral integrase in complex with its cofactor, where the observed translocation vector does not equal a small integral fraction of a unit-cell edge, is reported and its general application to all classic LTD cases is predicted. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698868 Thu, 13 Aug 2009 23:00:00 +0100 2698868 http://www.medworm.com/index.php?rid=2698867&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5164 Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaus... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698867 Thu, 13 Aug 2009 23:00:00 +0100 2698867 http://www.medworm.com/index.php?rid=2698866&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5098 2,3-Diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1P enolase), a RuBisCO-like protein (RLP), catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate. The crystal structure of the apo decarbamylated form (E form) of Bacillus subtilis DK-MTP-1P enolase (Bs-DK-MTP-1P enolase) has been determined at 2.3 Å resolution. The overall structure of the E form of Bs-DK-MTP-1P enolase highly resembles that of Geobacillus kaustophilus DK-MTP-1P enolase (Gk-DK-MTP-1P enolase), with the exception of a few insertions or deletions and of a few residues at the active site. In the E form of Bs-DK-MTP-1P enolase, Lys150 (equivalent to Lys175 in RuBisCO) at the active site adopts a conformation that is distinct from those observed in the other forms of Gk-DK-MTP-1P enolase. This unusua... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698866 Thu, 13 Aug 2009 23:00:00 +0100 2698866 http://www.medworm.com/index.php?rid=2698865&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5129 Thioredoxins (Trxs) are protein disulfide reductases that regulate the intracellular redox environment and are important for seed germination in plants. Trxs are in turn regulated by NADPH-dependent thioredoxin reductases (NTRs), which provide reducing equivalents to Trx using NADPH to recycle Trxs to the active form. Here, the first crystal structure of a cereal NTR, HvNTR2 from Hordeum vulgare (barley), is presented, which is also the first structure of a monocot plant NTR. The structure was determined at 2.6 Å resolution and refined to an Rcryst of 19.0% and an Rfree of 23.8%. The dimeric protein is structurally similar to the structures of AtNTR-B from Arabidopsis thaliana and other known low-molecular-weight NTRs. However, the relative position of the two NTR cofactor-binding doma... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2698865 Thu, 13 Aug 2009 23:00:00 +0100 2698865 http://www.medworm.com/index.php?rid=2673854&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5125 A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 Å resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7 Å resolution. The protonation and deprotonation states of all of the charged amino-acid residues allowed us to provide a definitive description of the hydrogen-bonding network around the active site and the H atoms of the key His48 residue. Differences i... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2673854 Thu, 06 Aug 2009 12:11:39 +0100 2673854 http://www.medworm.com/index.php?rid=2673858&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5160 Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, they are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σA) weighted. Analysis shows that they are comparable and correspond better to the final model than σA and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebui... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2673858 Wed, 05 Aug 2009 23:00:00 +0100 2673858 http://www.medworm.com/index.php?rid=2673857&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5287 Microfluidics is a promising technology for the rapid identification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2 mm thin transparent cards which contain 500 chambers, each with a volume of 320 nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, includin... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2673857 Wed, 05 Aug 2009 23:00:00 +0100 2673857 http://www.medworm.com/index.php?rid=2673856&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5015 In the last decade, advances in instrumentation and software development have made crystallography a powerful tool in structural biology. Using this method, structural information can now be acquired from pathological crystals that would have been abandoned in earlier times. In this paper, the order–disorder (OD) structure of fluorescent protein FP480 is discussed. The structure is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, namely rotated 90° with respect to each other around the crystal c axis, with tetramer axes coincident with crystallographic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates a rotational OD structure with statistically averaged I422 symmetry, although the presence of ver... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2673856 Wed, 05 Aug 2009 23:00:00 +0100 2673856 http://www.medworm.com/index.php?rid=2673855&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5133 The controller protein of the Esp1396I restriction–modification (R–M) system binds differentially to three distinct operator sequences upstream of the methyltransferase (M) and endonuclease (R) genes to regulate the timing of gene expression. The crystal structure of a complex of the protein with two adjacent operator DNA sequences has been reported; however, the structure of the free protein has not yet been determined. Here, the crystal structure of the free protein is reported, with seven dimers in the asymmetric unit. Two of the 14 monomers show an alternative conformation to the major conformer in which the side chains of residues 43–46 in the loop region flanking the DNA-recognition helix are displaced by up to 10 Å. It is proposed that the adoption of these two conformation... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2673855 Wed, 05 Aug 2009 23:00:00 +0100 2673855 http://www.medworm.com/index.php?rid=2605370&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5130 Bacterial persistence is the ability of individual cells to randomly enter a period of dormancy during which the cells are protected against antibiotics. In Escherichia coli, persistence is regulated by the activity of a protein kinase HipA and its DNA-binding partner HipB, which is a strong inhibitor of both HipA activity and hip operon transcription. The crystal structure of the HipBA complex was solved by application of the SAD technique to a mercury derivative. In this article, the fortuitous and interesting effect of mercury soaks on the native HipBA crystals is discussed as well as the intriguing tryptophan-binding pocket found on the HipA surface. A HipA-regulation model is also proposed that is consistent with the available structural and biochemical data. (Source: Acta Crystallogr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605370 Thu, 16 Jul 2009 12:01:06 +0100 2605370 http://www.medworm.com/index.php?rid=2605369&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5131 Protein crystallography has proven to be an effective method of obtaining high-resolution structures of protein–ligand complexes. However, in certain cases only apoprotein structures are readily available and the generation of crystal complexes is more problematic. Some crystallographic systems are not amenable to soaking of ligands owing to crystal-packing effects and many protein–ligand complexes do not crystallize under the same conditions as used for the apoprotein. Using crystals of human phosphodiesterase 10a (hPDE10a) as an example of such a challenging crystallographic system, the structure of the complex with papaverine was obtained to 2.8 Å resolution using protein crystals cross-linked by glutaraldehyde prior to soaking of the ligand. Inspection of the electron-density ma... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605369 Thu, 16 Jul 2009 12:01:06 +0100 2605369 http://www.medworm.com/index.php?rid=2605368&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5011 The integrin α6β4 is a receptor for laminins and provides stable adhesion of epithelial cells to the basement membranes. In addition, α6β4 is important for keratinocyte migration during wound healing and favours the invasion of carcinomas into surrounding tissue. The cytoplasmic domain of the β4 subunit is responsible for most of the intracellular interactions of the integrin; it contains four fibronectin type III domains and a Calx-β motif. The crystal structure of the Calx-β domain of β4 was determined to 1.48 Å resolution. The structure does not contain cations and biophysical data support the supposition that the Calx-β domain of β4 does not bind calcium. Comparison of the Calx-β domain of β4 with the calcium-binding domains of Na+/Ca2+-exchanger 1 reveals that in β4 A... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605368 Thu, 16 Jul 2009 12:01:06 +0100 2605368 http://www.medworm.com/index.php?rid=2605367&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5362 Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The kcat values and Km values are (2.54 ± 0.19) × 105 min−1 and 0.39 ± 0.049 mM, respectively, for the wild type; (3.72 ± 0.28) × 103 min−1 and 2.18 ± 0.028 mM, respectively, for the F96S mutant; (1.11 ± 0.03) × 104 min−1 and 2.62 ± 0.042 mM, respectively, for the F96H mutant; and (1.4... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605367 Thu, 16 Jul 2009 12:01:06 +0100 2605367 http://www.medworm.com/index.php?rid=2605366&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5162 In this report, a conserved C-terminal domain (∼100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8 Å resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P43. The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly α-helical content displaying a unique fold that could be engaged in protein–... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605366 Thu, 16 Jul 2009 12:01:06 +0100 2605366 http://www.medworm.com/index.php?rid=2605365&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5128 Antimicrobial drug resistance is a serious public health problem and the development of new antibiotics has become an important priority. Ristocetin A is a class III glycopeptide antibiotic that is used in the diagnosis of von Willebrand disease and which has served as a lead compound for the development of new antimicrobial therapeutics. The 1.0 Å resolution crystal structure of the complex between ristocetin A and a bacterial cell-wall peptide has been determined. As is observed for most other glycopeptide antibiotics, it is shown that ristocetin A forms a back-to-back dimer containing concave binding pockets that recognize the cell-wall peptide. A comparison of the structure of ristocetin A with those of class I glycopeptide antibiotics such as vancomycin and balhimycin identifies d... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605365 Thu, 16 Jul 2009 12:01:06 +0100 2605365 http://www.medworm.com/index.php?rid=2605364&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5159 This study reveals the striking potential of these complexes for SAD phasing using a laboratory source and further reinforces their relevance for high-throughput macromolecular crystallography. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605364 Thu, 16 Jul 2009 12:01:05 +0100 2605364 http://www.medworm.com/index.php?rid=2605363&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5127 Aminopeptidase N (APN; EC 3.4.11.2) purified from Escherichia coli has been crystallized with the optically pure aminophosphinic inhibitor PL250, H3N+-CH(CH3)-P(O)(OH)-CH2-CH(CH2Ph)-CONH-CH(CH2Ph)CO2−, which mimics the transition state of the hydrolysis reaction. PL250 inhibits APN with a Ki of 1.5–2.2 nM and its three-dimensional structure in complex with E. coli APN showed its interaction with the S1, S′1 and S′2 subsites of the catalytic site. In this structure, the Zn ion was shown to be pentacoordinated by His297, His301 and Glu320 of APN and the two O atoms of the phosphinic moiety of PL250. One of these O atoms is also involved in a hydrogen bond to Tyr381, supporting the proposed role of this amino acid in the stabilization of the transition state of the enzymatic process... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605363 Thu, 16 Jul 2009 12:01:05 +0100 2605363 http://www.medworm.com/index.php?rid=2605362&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5027 In order to elucidate the relationship between the stability and the structure of the monohaem cytochrome c555 (AA c555) from the hyperthermophilic bacterium Aquifex aeolicus, chemical denaturation and crystal structure determination were carried out. AA c555 exhibited higher stability than the thermophilic Hydrogenobacter thermophilus cytochrome c552 (HT c552), which is one of the most stable cytochromes c. The three-dimensional crystal structure of AA c555, which was determined using the multiple anomalous dispersion technique at 1.15 Å resolution, included a unique 14-residue extra helix, while the side-chain interactions of several amino-acid residues responsible for the stability of HT c552 were conserved in AA c555. The side chain of the Met61 residue in the extra helix was aligne... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2605362 Thu, 16 Jul 2009 12:01:05 +0100 2605362 http://www.medworm.com/index.php?rid=2587621&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5023 Parvalbumins (PVs) are calcium-buffer proteins that belong to the EF-hand family. Their N-terminal domain consists of two antiparallel helices A and B that make up a flat hydrophobic surface that is associated with the opposite side of the CD and EF binding sites. A single conserved Arg75–Glu81 salt bridge is buried in this hydrophobic interface. The structure of a rat PV mutant in which Arg75 was replaced by alanine was solved by molecular replacement. Unexpectedly, a large distance deviation of 7.8 Å was observed for the AB loop but not for the residues that flank the R75A mutation. The thermal stability of the calcium-loaded form is lower (Tm = 352.0 K; ΔTm = −11.4 K) than that of the wild-type protein and the apo mutant is unfolded at room temperature. Weaker calcium or ma... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587621 Fri, 10 Jul 2009 12:05:51 +0100 2587621 http://www.medworm.com/index.php?rid=2587628&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5025 The Modoc virus (MODV) is a flavivirus with no known vector (NKV). Evolutionary studies have shown that the viruses in the MODV group have evolved in association with mammals (bats, rodents) without transmission by an arthropod vector. MODV methyltransferase is the first enzyme from this evolutionary branch to be structurally characterized. The high-resolution structure of the methyltransferase domain of the MODV NS5 protein (MTaseMODV) was determined. The protein structure was solved in the apo form and in complex with its cofactor S-adenosyl-l-methionine (SAM). Although it belongs to a separate evolutionary branch, MTaseMODV shares structural characteristics with flaviviral MTases from the other branches. Its capping machinery is a relatively new target in flaviviral drug development and... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587628 Thu, 09 Jul 2009 23:00:00 +0100 2587628 http://www.medworm.com/index.php?rid=2587627&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5021 Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPAR subtypes display different tissue distribution patterns and distinct pharmacological profiles, they all are essentially related to fatty-acid and glucose metabolism. Since the PPARs share similar three-dimensional structures within the LBDs, synthetic ligands which simultaneously activate two or all of the PPARs could be potent candidates in terms of drugs for the treatment of abnormal metabolic homeostasis. The structures of several PPAR LBDs were determined in complex with synthetic ligands, derivatives of 3-(4-alkoxyphenyl)propanoic acid, ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587627 Thu, 09 Jul 2009 23:00:00 +0100 2587627 http://www.medworm.com/index.php?rid=2587626&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5355 The p38 mitogen-activated protein kinases are activated in response to environmental stress and cytokines and play a significant role in transcriptional regulation and inflammatory responses. Of the four p38 isoforms known to date, two (p38α and p38β) have been identified as targets for cytokine-suppressive anti-inflammatory drugs. Recently, it was reported that specific inhibition of the p38α isoform is necessary and sufficient for anti-inflammatory efficacy in vivo, while further inhibition of p38β may not provide any additional benefit. In order to aid the development of p38α-selective compounds, the three-dimensional structure of p38β was determined. To do so, the C162S and C119S,C162S mutants of human MAP kinase p38β were cloned, expressed in Escherichia coli and purified. Ini... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587626 Thu, 09 Jul 2009 23:00:00 +0100 2587626 http://www.medworm.com/index.php?rid=2587625&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5142 TTHA1846 is a conserved hypothetical protein from Thermus thermophilus HB8 with a molecular mass of 15.1 kDa that belongs to the thioesterase superfamily (Pfam 03061). Here, the 1.9 Å resolution crystal structure of TTHA1846 from T. thermophilus is reported. The crystal structure is a dimer of dimers. Each subunit adopts the so-called hot-dog fold composed of five antiparallel β-strands flanked on one side by a rather long α-helix and shares structural similarity to a number of thioesterases. Unexpectedly, TTHA1846 binds one metal ion and one ligand per subunit. The ligand density was modelled as coenzyme A (CoA). Its structure was confirmed by MALDI–TOF mass spectrometry and electron-density mapping. X-ray absorption fine-structure (XAFS) measurement of the crystal unambiguously... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587625 Thu, 09 Jul 2009 23:00:00 +0100 2587625 http://www.medworm.com/index.php?rid=2587624&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmh5019 Intercellular signalling is an essential characteristic of multicellular organisms. Gap junctions, which consist of arrays of intercellular channels, permit the exchange of ions and small molecules between adjacent cells. Here, the structural determination of a gap junction channel composed of connexin 26 (Cx26) at 3.5 Å resolution is described. During each step of the purification process, the protein was examined using electron microscopy and/or dynamic light scattering. Dehydration of the crystals improved the resolution limits. Phase refinement using multi-crystal averaging in conjunction with noncrystallographic symmetry averaging based on strictly determined noncrystallographic symmetry operators resulted in an electron-density map for model building. The amino-acid sequence of a ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587624 Thu, 09 Jul 2009 23:00:00 +0100 2587624 http://www.medworm.com/index.php?rid=2587623&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5126 Iclaprim is a novel dihydrofolate reductase (DHFR) inhibitor belonging to the 2,4-diaminopyrimidine class of antibiotics, of which trimethoprim (TMP) is the most well known representative. Iclaprim exhibits potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) phenotypes, including TMP-resistant strains. The inhibition properties of racemic iclaprim and of the two enantiomers, termed AR-101 and AR-102, towards S. aureus wild-type DHFR and TMP-resistant F98Y mutant DHFR were determined and compared. Similar to TMP, AR-101, AR-102 and iclaprim are all competitive inhibitors with respect to the substrate dihydrofolate. Iclaprim, AR-101 and AR-102 demonstrated little or no diff... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587623 Thu, 09 Jul 2009 23:00:00 +0100 2587623 http://www.medworm.com/index.php?rid=2587622&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5099 The production of biofuels using biomass is an alternative route to support the growing global demand for energy and to also reduce the environmental problems caused by the burning of fossil fuels. Cellulases are likely to play an important role in the degradation of biomass and the production of sugars for subsequent fermentation to fuel. Here, the crystal structure of an endoglucanase, Cel9A, from Alicyclobacillus acidocaldarius (Aa_Cel9A) is reported which displays a modular architecture composed of an N-terminal Ig-like domain connected to the catalytic domain. This paper describes the overall structure and the detailed contacts between the two modules. Analysis suggests that the interaction involving the residues Gln13 (from the Ig-like module) and Phe439 (from the catalytic module) i... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2587622 Thu, 09 Jul 2009 23:00:00 +0100 2587622 http://www.medworm.com/index.php?rid=2555457&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0389 The resolution gap between macromolecular crystallography and electron microscopy continues to decrease. Recent advances in specimen preparation, instrumentation and computational power have allowed accurate structure determination of larger macromolecular complexes by crystallography and/or by electron microscopy on cryovitrified samples. New possibilities in structural biology have opened up and new challenges are faced to further reduce the resolution gap. A workshop at the Lorentz Center, Leiden, The Netherlands, which took place in May 2008, was organized to push further the limits of both complementary techniques through improved computational methods. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555457 Tue, 30 Jun 2009 16:26:59 +0100 2555457 http://www.medworm.com/index.php?rid=2555469&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5144 Mannose-6-phosphate isomerase (MPI) catalyzes the interconversion of mannose 6-phosphate and fructose 6-phosphate. X-ray crystal structures of MPI from Salmonella typhimurium in the apo form (with no metal bound) and in the holo form (with bound Zn2+) and two other structures with yttrium bound at an inhibitory site and complexed with Zn2+ and fructose 6-phosphate (F6P) were determined in order to gain insights into the structure and the isomerization mechanism. Isomerization involves acid/base catalysis with proton transfer between the C1 and C2 atoms of the substrate. His99, Lys132, His131 and Asp270 are close to the substrate and are likely to be the residues involved in proton transfer. The interactions observed at the active site suggest that the ring-opening step is probably catalyze... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555469 Fri, 19 Jun 2009 23:00:00 +0100 2555469 http://www.medworm.com/index.php?rid=2555468&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5123 Three anionic salmon trypsin isoforms (CST-1, CST-2 and CST-3) were isolated from the pyloric caeca of chum salmon (Oncorhynchus keta). The order of catalytic efficiency (Km/kcat) of the isoforms during BAPA hydrolysis was CST-2 > CST-1 > CST-3. In order to find a structural rationalization for the observed difference in catalytic efficiency, the X-ray crystallographic structures of the three isoforms were compared in detail. Some structural differences were observed in the C-terminal α-helix, interdomain loop and active-site region. From the results of the detailed comparison, it appears that the structural flexibility of the C-terminal α-helix, which interacts with the N-terminal domain, and the substrate-binding pocket in CST-3 are lower than those in CST-1 and CST-2. In addition, t... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555468 Fri, 19 Jun 2009 23:00:00 +0100 2555468 http://www.medworm.com/index.php?rid=2555467&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5125 The flagellate protozoan parasite Trypanosoma cruzi is the pathogenic agent of Chagas disease (also called American trypanosomiasis), which causes approximately 50 000 deaths annually. The disease is endemic in South and Central America. The parasite is usually transmitted by a blood-feeding insect vector, but can also be transmitted via blood transfusion. In the chronic form, Chagas disease causes severe damage to the heart and other organs. There is no satisfactory treatment for chronic Chagas disease and no vaccine is available. There is an urgent need for the development of chemotherapeutic agents for the treatment of T. cruzi infection and therefore for the identification of potential drug targets. The dihydrofolate reductase activity of T. cruzi, which is expressed as part of a bif... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555467 Fri, 19 Jun 2009 23:00:00 +0100 2555467 http://www.medworm.com/index.php?rid=2555466&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5100 The room-temperature X-ray structures of ubiquitin (PDB code 1ubq) and of the RNA-binding domain of nonstructural protein 1 of influenza A virus (PDB code 1ail) solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and Rfree factors similar to those of the deposited X-ray structure, the 13Cα chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of con... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555466 Fri, 19 Jun 2009 23:00:00 +0100 2555466 http://www.medworm.com/index.php?rid=2555465&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5060 A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 Å is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can be employed for subsequent phase extension to higher resolution. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555465 Fri, 19 Jun 2009 23:00:00 +0100 2555465 http://www.medworm.com/index.php?rid=2555464&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5059 The fitting of high-resolution structures into low-resolution densities obtained from techniques such as electron microscopy or small-angle X-ray scattering can yield powerful new insights. While several algorithms for achieving optimal fits have recently been developed, relatively little effort has been devoted to developing objective measures for judging the quality of the resulting fits, in particular with regard to the danger of overfitting. Here, a general method is presented for obtaining confidence intervals for atomic coordinates resulting from fitting of atomic resolution domain structures into low-resolution densities using well established statistical tools. It is demonstrated that the resulting confidence intervals are sufficiently accurate to allow meaningful statistical tests... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555464 Fri, 19 Jun 2009 23:00:00 +0100 2555464 http://www.medworm.com/index.php?rid=2555463&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5054 An expectation-maximization algorithm for maximum-likelihood refinement of electron-microscopy images is presented that is based on fitting mixtures of multivariate t-distributions. The novel algorithm has intrinsic characteristics for providing robustness against atypical observations in the data, which is illustrated using an experimental test set with artificially generated outliers. Tests on experimental data revealed only minor differences in two-dimensional classifications, while three-dimensional classification with the new algorithm gave stronger elongation factor G density in the corresponding class of a structurally heterogeneous ribosome data set than the conventional algorithm for Gaussian mixtures. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555463 Fri, 19 Jun 2009 23:00:00 +0100 2555463 http://www.medworm.com/index.php?rid=2555462&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5056 Most known methods for the determination of the structure of macromolecular complexes are limited or at least restricted at some point by their computational demands. Recent developments in information technology such as multicore, parallel and GPU processing can be used to overcome these limitations. In particular, graphics processing units (GPUs), which were originally developed for rendering real-time effects in computer games, are now ubiquitous and provide unprecedented computational power for scientific applications. Each parallel-processing paradigm alone can improve overall performance; the increased computational performance obtained by combining all paradigms, unleashing the full power of today's technology, makes certain applications feasible that were previously virtually impo... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555462 Fri, 19 Jun 2009 23:00:00 +0100 2555462 http://www.medworm.com/index.php?rid=2555461&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5057 Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in r... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555461 Fri, 19 Jun 2009 23:00:00 +0100 2555461 http://www.medworm.com/index.php?rid=2555460&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5055 Molecular replacement can fail to find a solution, namely a unique orientation and position of a search model, even when many search models are tested under various conditions. Simultaneous use of the results of these searches may help in the solution of such difficult structures. A closeness between the peaks of several calculated rotation functions may identify the model orientation. The largest and most compact cluster of such peaks usually corresponds to models which are oriented similarly to the molecule under study. A search for the optimal translation may be more problematic and both individual translation functions and straightforward cluster analysis in the space of geometric parameters such as rotation angles and translation vectors may give no result. An improvement may be obtai... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555460 Fri, 19 Jun 2009 23:00:00 +0100 2555460 http://www.medworm.com/index.php?rid=2555459&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fic5058 The structural refinement of large complexes at the lower resolution limit is often difficult and inefficient owing to the limited number of reflections and the frequently high-level structural flexibility. A new normal-mode-based X-ray crystallographic refinement method has recently been developed that enables anisotropic B-factor refinement using a drastically smaller number of thermal parameters than even isotropic refinement. Here, the method has been systematically tested on a total of eight systems in the resolution range 3.0–3.9 Å. This series of tests established the most applicable scenarios for the method, the detailed procedures for its application and the degree of structural improvement. The results demonstrated substantial model improvement at the lower resolution limit,... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555459 Fri, 19 Jun 2009 23:00:00 +0100 2555459 http://www.medworm.com/index.php?rid=2555458&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5143 Unit-cell determination is the first step towards the structure solution of an unknown crystal form. Standard procedures for unit-cell determination cannot cope with data collections that consist of single diffraction patterns of multiple crystals, each with an unknown orientation. However, for beam-sensitive nanocrystals these are often the only data that can be obtained. An algorithm for unit-cell determination that uses randomly oriented electron-diffraction patterns with unknown angular relationships is presented here. The algorithm determined the unit cells of mineral, pharmaceutical and protein nanocrystals in orthorhombic high- and low-symmetry space groups, allowing (well oriented) patterns to be indexed. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2555458 Fri, 19 Jun 2009 23:00:00 +0100 2555458 http://www.medworm.com/index.php?rid=2413019&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5123 In this study, previous structural work is built upon by reporting the X-ray structures of DraE bound to two chloramphenicol derivatives: chloramphenicol succinate (CLS) and bromamphenicol (BRM). The CLS structure demonstrates that acylation of the 3-hydroxyl group of CLM with succinyl does not significantly perturb the mode of binding, while the BRM structure implies that the binding pocket is able to accommodate bulkier substituents on the N-acyl group. It is concluded that modifications of the 3-hydroxyl group would generate a potent Dr haemagglutinin inhibitor that would not cause the toxic side effects that are associated with the normal bacteriostatic activity of CLM. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413019 Sat, 16 May 2009 03:45:03 +0100 2413019 http://www.medworm.com/index.php?rid=2413030&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5155 The crystal structure of Plasmodium falciparum nucleosome assembly protein (PfNapL) was determined by iodide-SAD/SIRAS phasing methods using iodide-SAD data to 3.0 Å resolution and native data to 2.4 Å resolution. Halide-derivatized PfNapL crystals were obtained using the quick cryo-soaking method in which the native crystals were soaked in a cryosolution consisting of 500 mM NaI for a short period of 30–60 s and data were collected at an in-house X-ray source using Cu Kα radiation. Despite a low anomalous signal-to-noise ratio of 3.5 Å resolution bin, the data were sufficient to determine the structure by SAD/SIR/SIRAS methods using the soaked iodides. Previously, structure solution had failed with both molecular-replacement and selenomethionine-derivatization techniques... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413030 Fri, 15 May 2009 04:00:00 +0100 2413030 http://www.medworm.com/index.php?rid=2413029&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5156 This paper describes the structural analysis of the native form of laccase from Trametes hirsuta at 1.8 Å resolution. This structure provides a basis for the elucidation of the mechanism of catalytic action of these ubiquitous proteins. The 1.8 Å resolution native structure provided a good level of structural detail compared with many previously reported laccase structures. A brief comparison with the active sites of other laccases is given. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413029 Fri, 15 May 2009 04:00:00 +0100 2413029 http://www.medworm.com/index.php?rid=2413028&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5126 Archaeal RadAs are close homologues of eukaryal Rad51s (∼40% sequence identity). These recombinases promote ATP hydrolysis and a hallmark strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. Pairing of the 3′-overhangs located at the damaged DNA with a homologous double-stranded DNA enables the re-synthesis of the damaged region using the homologous DNA as the template. In recent studies, conformational changes in the DNA-interacting regions of Methanococcus voltae RadA have been correlated with the presence of activity-stimulating potassium or calcium ions in the ATPase centre. The series of crystal structures of M. maripaludis RadA presented here further suggest the conservation of an allosteric switch in the ATPase centre which controls th... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413028 Fri, 15 May 2009 04:00:00 +0100 2413028 http://www.medworm.com/index.php?rid=2413027&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fea5095 Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413027 Fri, 15 May 2009 04:00:00 +0100 2413027 http://www.medworm.com/index.php?rid=2413026&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5124 This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413026 Fri, 15 May 2009 04:00:00 +0100 2413026 http://www.medworm.com/index.php?rid=2413025&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftm5033 X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientatio... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413025 Fri, 15 May 2009 04:00:00 +0100 2413025 http://www.medworm.com/index.php?rid=2413024&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5026 Eukaryotic proliferating cell nuclear antigen (PCNA) is an essential replication accessory factor that interacts with a variety of proteins involved in DNA replication and repair. Each monomer of PCNA has an N-terminal domain A and a C-terminal domain B. In the structure of the wild-type PCNA protein, domain A of one monomer interacts with domain B of a neighboring monomer to form a ring-shaped trimer. Glu113 is a conserved residue at the subunit interface in domain A. Two distinct X-ray crystal structures have been determined of a mutant form of PCNA with a substitution at this position (E113G) that has previously been studied because of its effect on translesion synthesis. The first structure was the expected ring-shaped trimer. The second structure was an unanticipated nontrimeric form ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413024 Fri, 15 May 2009 04:00:00 +0100 2413024 http://www.medworm.com/index.php?rid=2413023&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5158 Rotation photographs can be readily indexed if enough candidate Bragg spots are identified to properly sample the reciprocal lattice. However, while automatic indexing algorithms are widely used for macromolecular data processing, they can produce incorrect results in special situations where a subset of Bragg spots is systematically overlooked. This is a potential outcome in cases where a noncrystallographic translational symmetry operator closely mimics an exact crystallographic translation. In these cases, a visual inspection of the diffraction image will reveal alternating strong and weak reflections. However, reliable detection of the weak-intensity reflections by software requires a systematic search for a diffraction signal targeted at specific reciprocal-space locations calculated ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413023 Fri, 15 May 2009 04:00:00 +0100 2413023 http://www.medworm.com/index.php?rid=2413022&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhm5074 (S)-Mandelate dehydrogenase (MDH) from Pseudomonas putida, a membrane-associated flavoenzyme, catalyzes the oxidation of (S)-mandelate to benzoylformate. Previously, the structure of a catalytically similar chimera, MDH-GOX2, rendered soluble by the replacement of its membrane-binding segment with the corresponding segment of glycolate oxidase (GOX), was determined and found to be highly similar to that of GOX except within the substituted segments. Subsequent attempts to cocrystallize MDH-GOX2 with substrate proved unsuccessful. However, the G81A mutants of MDH and of MDH-GOX2 displayed ∼100-fold lower reactivity with substrate and a modestly higher reactivity towards molecular oxygen. In order to understand the effect of the mutation and to identify the mode of substrate binding in MDH... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413022 Fri, 15 May 2009 04:00:00 +0100 2413022 http://www.medworm.com/index.php?rid=2413021&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5006 An algorithm is described which simulates a data set obtained from a protein crystal using the rotation method. The diffraction pattern of an ideal crystal is specified by the orientation of the crystal's cell axes with respect to a specified laboratory coordinate system, the distance between the crystal and the detector, the wavelength and the rotation range per frame. However, a realistic simulation of an experiment additionally requires at least a plausible physical model for crystal mosaicity and beam properties. To explore the physical basis of reflection shape and rocking-curve variation, the algorithm simulates the diffraction of a real crystal composed of mosaic blocks which is illuminated with a beam of given divergence and dispersion. Ray tracing for each reflection leads to refl... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413021 Fri, 15 May 2009 04:00:00 +0100 2413021 http://www.medworm.com/index.php?rid=2413020&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fyt5014 The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0 Å resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary appr... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2413020 Fri, 15 May 2009 04:00:00 +0100 2413020 http://www.medworm.com/index.php?rid=2339877&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbe5120 The nasal mucosa is a specialist interfacial region sandwiched between the olfactory system and the gaseous chemical milieu. In mammals and insects, this region is rich in odorant-binding proteins that are thought to aid olfaction by assisting mass transfer of the many different organoleptic compounds that make up the olfactory landscape. However, in mammals at least, our grasp on the exact function of odorant-binding proteins is tentative and better insight into the role of these proteins is warranted, not least because of their apparent significance in the olfactory systems of insects. Here, the crystal structure of rat odorant-binding protein 1 is reported at 1.6 Å resolution. This protein is one of the best-characterized mammalian odorant-binding proteins and only the third such pro... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339877 Sat, 18 Apr 2009 18:02:13 +0100 2339877 http://www.medworm.com/index.php?rid=2339888&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5012 Marked-up sequence alignments typically provide the central figure in articles describing proteins, whether in the fields of biochemistry, bioinformatics or structural biology. The generation of these figures is often unwieldy: interactive programs are often aesthetically limited and the use of batch programs requires the repetitive iterative editing of scripts. ALINE is a portable interactive graphical sequence-alignment editor implemented in Perl/Tk which produces publication-quality sequence-alignment figures where `what you see is what you get'. ALINE is freely available for download from http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/. (Source: Acta Crystallographica Section D) Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339888 Sat, 18 Apr 2009 04:00:00 +0100 2339888 http://www.medworm.com/index.php?rid=2339887&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Flv5004 The integrity and X-ray diffraction quality of protein crystals depend on the three-dimensional order of relatively weak but reproducible intermolecular contacts. Despite their importance, relatively little attention has been paid to the chemical and physical nature of these contacts, which are often regarded as stochastic and thus not different from randomly selected protein surface patches. Here, logistic regression was used to analyze crystal contacts in a database of 821 unambiguously monomeric proteins with structures determined to 2.5 Å resolution or better. It is shown that the propensity of a surface residue for incorporation into a crystal contact is not a linear function of its solvent-accessible surface area and that amino acids with low exposed surfaces, which are typically... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339887 Sat, 18 Apr 2009 04:00:00 +0100 2339887 http://www.medworm.com/index.php?rid=2339886&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5152 Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor (∼−300 kJ mol−1 for —COO− in non-aromatic inhibitors, ∼−120–210 kJ mol−1 for —CO... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339886 Sat, 18 Apr 2009 04:00:00 +0100 2339886 http://www.medworm.com/index.php?rid=2339885&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5157 Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249–256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339885 Sat, 18 Apr 2009 04:00:00 +0100 2339885 http://www.medworm.com/index.php?rid=2339884&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fmv5022 This study presents the structures of HP67 and its pH-stabilized mutant (H41Y) in a different crystal form and space group. For both constructs, two molecules are found in each asymmetric unit in the new space group P61. While one of the two structures (Mol A) is structurally similar to our previously determined structure (Mol X), the other (Mol B) has significant deviations, especially in the N-terminal subdomain, where lattice contacts do not appear to contribute to the difference. In addition, the structurally most different crystal structure, Mol B, is actually closer to the averaged NMR structure. Harmonic motions, as suggested by the B-factor profiles, differ between these crystal structures; crystal structures from the same space group share a similar pattern. Thus, heterogeneity an... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339884 Sat, 18 Apr 2009 04:00:00 +0100 2339884 http://www.medworm.com/index.php?rid=2339883&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5278 The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane–dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 Å resolution; their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modifica... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339883 Sat, 18 Apr 2009 04:00:00 +0100 2339883 http://www.medworm.com/index.php?rid=2339882&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5356 Inhibition of acetyl-CoA carboxylase (ACC) may prevent lipid-induced insulin resistance and type 2 diabetes, making the enzyme an attractive pharmaceutical target. Although the enzyme is highly conserved amongst animals, only the yeast enzyme structure is available for rational drug design. The use of biophysical assays has permitted the identification of a specific C-terminal truncation of the 826-residue human ACC2 carboxyl transferase (CT) domain that is both functionally competent to bind inhibitors and crystallizes in their presence. This C-terminal truncation led to the determination of the human ACC2 CT domain–CP-640186 complex crystal structure, which revealed distinctions from the yeast-enzyme complex. The human ACC2 CT-domain C-terminus is comprised of three intertwined α-heli... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339882 Sat, 18 Apr 2009 04:00:00 +0100 2339882 http://www.medworm.com/index.php?rid=2339881&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5154 Sulfur single-wavelength anomalous dispersion (S-SAD) and halide-soaking methods are increasingly being used for ab initio phasing. With the introduction of in-house Cr X-ray sources, these methods benefit from the enhanced anomalous scattering of S and halide atoms, respectively. Here, these methods were combined to determine the crystal structure of BsDegV, a DegV protein-family member from Bacillus subtilis. The protein was cocrystallized with bromide and low-redundancy data were collected to 2.5 Å resolution using Cr Kα radiation. 17 heavy-atom sites (ten sulfurs and seven bromides) were located using standard methods. The anomalous scattering of some of the BsDegV S atoms and Br atoms was weak, thus neither sulfurs nor bromides could be used alone for structure determination usi... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339881 Sat, 18 Apr 2009 04:00:00 +0100 2339881 http://www.medworm.com/index.php?rid=2339880&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5153 Glucocorticoid-induced TNF receptor ligand (GITRL), a prominent member of the TNF superfamily, activates its receptor on both effector and regulatory T cells to generate critical costimulatory signals that have been implicated in a wide range of T-cell immune functions. The crystal structures of murine and human orthologs of GITRL recombinantly expressed in Escherichia coli have previously been determined. In contrast to all classical TNF structures, including the human GITRL structure, murine GITRL demonstrated a unique `strand-exchanged' dimeric organization. Such a novel assembly behavior indicated a dramatic impact on receptor activation as well as on the signaling mechanism associated with the murine GITRL costimulatory system. In this present work, the 1.8 Å resolution crystal str... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339880 Sat, 18 Apr 2009 04:00:00 +0100 2339880 http://www.medworm.com/index.php?rid=2339879&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fdz5145 The signal recognition particle (SRP) Alu domain has been implicated in translation elongation arrest in yeasts and mammals. Fission yeast SRP RNA is similar to that of mammals, but has a minimal Alu-domain RNA lacking two stem-loops. The mammalian Alu-domain proteins SRP9 and SRP14 bind their cognate Alu RNA as a heterodimer. However, in yeasts, notably Saccaromyces cerevisiae, SRP14 is thought to bind Alu RNA as a homodimer, the SRP9 protein being replaced by SRP21, the function of which is not yet clear. Structural characterization of the Schizosaccharomyces pombe Alu domain may thus help to identify the critical features required for elongation arrest. Here, the crystal structure of the SRP14 subunit of S. pombe SRP (SpSRP14) which crystallizes as a homodimer, is presented. Comparison ... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339879 Sat, 18 Apr 2009 04:00:00 +0100 2339879 http://www.medworm.com/index.php?rid=2339878&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5108 Many Gram-negative bacteria use the chaperone–usher pathway to express adhesive surface structures, such as fimbriae, in order to mediate attachment to host cells. Periplasmic chaperones are required to shuttle fimbrial subunits or pilins through the periplasmic space in an assembly-competent form. The chaperones cap the hydrophobic surface of the pilins through a donor-strand complementation mechanism. FaeE is the periplasmic chaperone required for the assembly of the F4 fimbriae of enterotoxigenic Escherichia coli. The FaeE crystal structure shows a dimer formed by interaction between the pilin-binding interfaces of the two monomers. Dimerization and tetramerization have been observed previously in crystal structures of fimbrial chaperones and have been suggested to serve as a self-cap... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2339878 Sat, 18 Apr 2009 04:00:00 +0100 2339878 http://www.medworm.com/index.php?rid=2283174&cid=s_37342_60_f&fid=37342&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5345 Profilins are key regulators of the actin microfilament system and in neuronal tissues the profilin 2a isoform is the most abundant and important profilin. The high-resolution crystal structure of rat profilin 2a has been determined in the absence of ligands. By comparing the structure with those of peptide-liganded profilin 2a and unliganded profilin 2b, it can be concluded that the binding site for proline-rich peptides is pre-organized. The C-terminus of profilin 2a is also well ordered in the absence of ligand peptide, in contrast to the 2b isoform which is generated by alternative splicing. Covalent modifications of four cysteine residues were also detected in profilin 2a, as well as a number of other modifications in profilin 2 from rat brain; such modifications could significantly a... Acta Crystallographica Section D journals http://www.medworm.com/rss/comments.php?id=2283174 Sun, 22 Mar 2009 16:33:34 +0100 2283174