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 F' source. Sun, 21 Mar 2010 16:57:28 +0100 http://www.medworm.com/index.php?rid=3334616&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5125 SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein–protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 fami... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3334616 Fri, 05 Mar 2010 00:00:00 +0100 3334616 http://www.medworm.com/index.php?rid=3334615&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5118 Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3334615 Fri, 05 Mar 2010 00:00:00 +0100 3334615 http://www.medworm.com/index.php?rid=3334614&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5121 The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3334614 Fri, 05 Mar 2010 00:00:00 +0100 3334614 http://www.medworm.com/index.php?rid=3334613&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5122 The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3334613 Fri, 05 Mar 2010 00:00:00 +0100 3334613 http://www.medworm.com/index.php?rid=3334612&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5123 Domains of unknown function (DUFs) are a large set of uncharacterized protein families that are found in the Pfam database. Here, the scale and growth of functionally uncharacterized families in biological databases are surveyed and the prospects for discovering their function are examined. In particular, the important role that structural genomics can play in identifying potential function is evaluated. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3334612 Fri, 05 Mar 2010 00:00:00 +0100 3334612 http://www.medworm.com/index.php?rid=3314349&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5124 The environment of individual tryptophans in known protein structures and the effectiveness of four commercial robotic UV microscopes to illuminate tryptophan-containing protein crystals by either tryptophan fluorescence (epi-illumination) or absorbance (transmission) are evaluated. In agreement with other studies, tryptophan residues are found on average to be largely buried in protein structures (with ∼84% of their surface area buried) and to be surrounded by partially polar microenvironments (with ∼43% of their surface area covered by polar residues), which suggests an inherent degree of fluorescence signal quenching. In bacterial genomes, up to one-third (∼18.5% on average) of open reading frames are deficient in tryptophan. In the laboratory, because of the attenuation of UV ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3314349 Sat, 27 Feb 2010 00:00:00 +0100 3314349 http://www.medworm.com/index.php?rid=3314348&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5288 Plasma-membrane Ca2+-ATPases (PMCAs) are calcium pumps that expel Ca2+ from eukaryotic cells to maintain overall Ca2+ homoeostasis and to provide local control of intracellular Ca2+ signalling. They are of major physiological importance, with different isoforms being essential, for example, for presynaptic and postsynaptic Ca2+ regulation in neurons, feedback signalling in the heart and sperm motility. In the resting state, PMCAs are autoinhibited by binding of their C-terminal (in mammals) or N-terminal (in plants) tail to two major intracellular loops. Activation requires the binding of calcium-bound calmodulin (Ca2+-CaM) to this tail and a conformational change that displaces the autoinhibitory tail from the catalytic domain. The complex between calmodulin and the regulatory domain of ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3314348 Sat, 27 Feb 2010 00:00:00 +0100 3314348 http://www.medworm.com/index.php?rid=3314347&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5338 Peroxiredoxin II was cloned from mouse B cells into pCold 1 expression vector and produced as a His-tagged recombinant protein in Escherichia coli. A ring form was isolated by gel filtration. A crystal obtained by the sitting-drop vapour-diffusion method diffracted to 1.77 Å resolution at 100 K. The crystal belonged to space group P21212, with unit-cell parameters a = 117.4, b = 133.9, c = 139.1 Å. The asymmetric unit is expected to contain six dimers of peroxiredoxin II, with a corresponding solvent content of 39.3%. Peaks in the native Patterson function together with pseudo-systematic absences suggested that the crystals suffered from severe translational pseudosymmetry. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3314347 Sat, 27 Feb 2010 00:00:00 +0100 3314347 http://www.medworm.com/index.php?rid=3314346&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5078 The oxygenase HpaB is a component of the 4-hydroxyphenylacetate 3-monooxygenase enzyme that is responsible for the hydroxylation of 4-hydroxyphenylacetate. It utilizes molecular oxygen and a reduced flavin, which is provided by HpaC, the second component of the enzyme. While isolating integral membrane respiratory complexes from Thermus thermophilus, microcrystals of HpaB were formed. Further purification of the enzyme was achieved by repetitive crystallization. Subsequently, well shaped single crystals of the native enzyme that diffract to 1.82 Å resolution were grown in sitting drops. They belong to the orthorhombic space group I222, with unit-cell parameters a = 91.3, b = 99.8, c = 131.7 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3314346 Sat, 27 Feb 2010 00:00:00 +0100 3314346 http://www.medworm.com/index.php?rid=3314345&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5098 Disaccharide phosphorylases are able to catalyze both the synthesis and the breakdown of disaccharides and have thus emerged as attractive platforms for tailor-made sugar synthesis. Cellobiose phosphorylase from Cellulomonas uda (CPCuda) is an enzyme that belongs to glycoside hydrolase family 94 and catalyzes the reversible breakdown of cellobiose [β-d-glucopyranosyl-(1,4)-d-glucopyranose] to α-d-glucose-1-phosphate and d-glucose. Crystals of ligand-free recombinant CPCuda and of its complexes with substrates and reaction products yielded complete X-ray diffraction data sets to high resolution using synchrotron radiation but suffered from significant variability in diffraction quality. In at least one case an intriguing space-group transition from a primitive monoclinic to a primitive o... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3314345 Sat, 27 Feb 2010 00:00:00 +0100 3314345 http://www.medworm.com/index.php?rid=3314344&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5404 Pyruvate dehydrogenase phosphatase (PDP) is a mitochondrial serine phosphatase that activates phosphorylated pyruvate dehydrogenase complex by dephosphorylation. In humans, two PDP isoforms (1 and 2) have been identified. PDP1 is composed of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r), whereas PDP2 consists of only a catalytic subunit (PDP2c). Both PDP1c and PDP2c have been crystallized individually and complete X-ray diffraction data sets have been collected to 2.45 and 2.0 Å resolution, respectively. The PDP1c crystals belonged to space group P41212 or P43212, with unit-cell parameters a = b = 65.1, c = 216.1 Å. The asymmetric unit is expected to contain one molecule, with a Matthews coefficient VM of 2.56 Å3 Da−1. The PDP2c crystals belonged to space group ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3314344 Sat, 27 Feb 2010 00:00:00 +0100 3314344 http://www.medworm.com/index.php?rid=3306086&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5052 The transcription factor FocB belongs to a family of regulators encoded by several different fimbriae gene clusters in uropathogenic Escherichia coli. Recent findings suggest that FocB-family proteins may form different protein–protein complexes and that they may exert both positive and negative effects on the transcription of fimbriae genes. However, little is known about the actual role and mode of action when these proteins interact with the fimbriae operons. The 109-amino-acid FocB transcription factor from the foc gene cluster in E. coli strain J96 has been cloned, expressed and purified. The His6-tagged fusion protein was captured by Ni2+-affinity chromatography, cleaved with tobacco etch virus protease and purified by gel filtration. The purified protein is oligomeric, most likely... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3306086 Thu, 25 Feb 2010 00:00:00 +0100 3306086 http://www.medworm.com/index.php?rid=3306085&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5047 Phosphoglucose isomerase (PGI) is a key enzyme in glycolysis and glycogenesis that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). For crystallographic studies, PGI from the human malaria parasite Plasmodium falciparum (PfPGI) was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.5 Å resolution were collected from an orthorhombic crystal form belonging to space group P212121 with unit-cell parameters a = 103.3, b = 104.1, c = 114.6 Å. Structural analysis by molecular replacement is in progress. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3306085 Thu, 25 Feb 2010 00:00:00 +0100 3306085 http://www.medworm.com/index.php?rid=3306084&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5046 The nonmevalonate pathway of isoprenoid biosynthesis present in Plasmodium falciparum is known to be an effective target for antimalarial drugs. The second enzyme of the nonmevalonate pathway, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), catalyzes the transformation of 1-deoxy-d-xylulose 5-phosphate (DXP) to 2-C-methyl-d-erythritol 4-phosphate (MEP). For crystallographic studies, DXR from the human malaria parasite P. falciparum (PfDXR) was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method in the presence of NADPH. X-ray diffraction data to 1.85 Å resolution were collected from a monoclinic crystal form belonging to space group C2 with unit-cell parameters a = 168.89, b = 59.65, c = 86.58 Å, β = 117.8°. Structural a... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3306084 Thu, 25 Feb 2010 00:00:00 +0100 3306084 http://www.medworm.com/index.php?rid=3306083&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5248 The multimodular scaffoldin subunit CipA is the central component of the cellulosome, a multienzyme plant cell-wall-degrading complex, from Clostridium thermocellum. It captures secreted cellulases and hemicellulases and anchors the entire complex to the cell surface via high-affinity calcium-dependent interactions between cohesin and dockerin modules termed type I and type II interactions. The crystallization of a heterotrimeric complex comprising the type II cohesin module from the cell-surface protein SdbA, a trimodular C-terminal fragment of the scaffoldin CipA and the type I dockerin module from the CelD cellulase is reported. The crystals belonged to space group P212121, with unit-cell parameters a = 119.37, b = 186.31, c = 191.17 Å. The crystals diffracted to 2.7 Å resolut... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3306083 Thu, 25 Feb 2010 00:00:00 +0100 3306083 http://www.medworm.com/index.php?rid=3306082&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fus5004 A1Ao ATP synthases are the major energy producers in archaea. Subunit E of the stator domain of the ATP synthase from Pyrococcus horikoshii OT3 was cloned, expressed and purified to homogeneity. The monodispersed protein was crystallized by vapour diffusion. A complete diffraction data set was collected to 3.3 Å resolution with 99.4% completeness using a synchrotron-radiation source. The crystals belonged to space group I4, with unit-cell parameters a = 112.51, b = 112.51, c = 96.25 Å, and contained three molecules in the asymmetric unit. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3306082 Thu, 25 Feb 2010 00:00:00 +0100 3306082 http://www.medworm.com/index.php?rid=3306081&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbo5073 Rice (Oryza sativa L.) Os4BGlu12, a glycoside hydrolase family 1 β-glucosidase (EC 3.2.1.21), was expressed as a fusion protein with an N-terminal thioredoxin/His6 tag in Escherichia coli strain Origami B (DE3) and purified with subsequent removal of the N-terminal tag. Native Os4BGlu12 and its complex with 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-d-glucopyranoside (DNP2FG) were crystallized using 19% polyethylene glycol (3350 or 2000, respectively) in 0.1 M Tris–HCl pH 8.5, 0.16 M NaCl at 288 K. Diffraction data sets for the apo and inhibitor-bound forms were collected to 2.50 and 2.45 Å resolution, respectively. The space group and the unit-cell parameters of the crystal indicated the presence of two molecules per asymmetric unit, with a solvent content of 50%. The structure of ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3306081 Thu, 25 Feb 2010 00:00:00 +0100 3306081 http://www.medworm.com/index.php?rid=3301488&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5245 Neelaredoxins are a type of superoxide reductase (SOR), which are blue 14 kDa metalloproteins with a catalytic nonhaem iron centre coordinated by four histidines and one cysteine in the ferrous form. Anaerobic organisms such as Archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, have developed defence mechanisms against toxic oxygen species in which superoxide reductases play a key role. SOR is responsible for scavenging toxic superoxide anion radicals (O2·−), catalysing the one-electron reduction of superoxide to hydrogen peroxide. Crystals of recombinant A. fulgidus neelaredoxin in the oxidized form (13.7 kDa, 125 residues) were obtained using polyethylene glycol and ammonium sulfate. These crystals diffracted to 1.9 Å resolution and belonged to the tetragona... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301488 Wed, 24 Feb 2010 00:00:00 +0100 3301488 http://www.medworm.com/index.php?rid=3301487&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5209 S-Adenosyl-l-homocysteine hydrolase (SAHH; EC 3.3.1.1) catalyzes the reversible hydrolysis of S-adenosyl-l-homocysteine to adenosine and l-homocysteine. For crystallographic investigations, mouse SAHH (MmSAHH) was overexpressed in bacterial cells and crystallized using the hanging-drop vapour-diffusion method in the presence of the reaction product adenosine. X-ray diffraction data to 1.55 Å resolution were collected from an orthorhombic crystal form belonging to space group I222 with unit-cell parameters a = 100.64, b = 104.44, c = 177.31 Å. Structural analysis by molecular replacement is in progress. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301487 Wed, 24 Feb 2010 00:00:00 +0100 3301487 http://www.medworm.com/index.php?rid=3301486&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5280 Chitosan is degraded to glucosamine (GlcN) by chitosanase and exo-β-d-glucosaminidase (GlcNase). GlcNase from Trichoderma reesei (Gls93) is a 93 kDa extracellular protein composed of 892 amino acids. The enzyme liberates GlcN from the nonreducing end of the chitosan chain in an exo-type manner and belongs to glycoside hydrolase family 2. For crystallographic investigations, Gls93 was overexpressed in Pichia pastoris cells. The recombinant Gls93 had two molecular forms of ∼105 kDa (Gls93-F1) and ∼100 kDa (Gls93-F2), with the difference between them being caused by N-glycosylation. Both forms were crystallized by the hanging-drop vapour-diffusion method. Crystals of Gls93-F1 belonged to the orthorhombic space group P212121, with unit-cell parameters a = 98.27, b = 98.42, c = 108... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301486 Wed, 24 Feb 2010 00:00:00 +0100 3301486 http://www.medworm.com/index.php?rid=3301485&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5283 In this study, a recombinant Trypanosoma brucei gambiense GK (rTbgGK) with an N-terminal cleavable His6 tag was overexpressed, purified to homogeneity and crystallized by the sitting-drop vapour-diffusion method using PEG 400 as a precipitant. A complete X-ray diffraction data set to 2.75 Å resolution indicated that the crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 63.84, b = 121.50, c = 154.59 Å. The presence of two rTbgGK molecules in the asymmetric unit gives a Matthews coefficient (VM) of 2.5 Å3 Da−1, corresponding to 50% solvent content. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301485 Wed, 24 Feb 2010 00:00:00 +0100 3301485 http://www.medworm.com/index.php?rid=3301484&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5247 Ferredoxin-NADP+ oxidoreductase encoded by Bacillus subtilis yumC has been purified and successfully crystallized in complex with NADP+ in two forms. Diffraction data from crystals of these two forms were collected at resolutions of 1.8 and 1.9 Å. The former belonged to space group P21212, with unit-cell parameters a = 63.90, b = 135.72, c = 39.19 Å, and the latter to space group C2, with unit-cell parameters a = 207.47, b = 64.85, c = 61.12 Å, β = 105.82°. The initial structure was determined by the molecular-replacement method using a thioredoxin reductase-like protein as a search model. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301484 Wed, 24 Feb 2010 00:00:00 +0100 3301484 http://www.medworm.com/index.php?rid=3301483&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5327 β-Galactosidase from Kluyveromyces lactis catalyses the hydrolysis of the β-galactosidic linkage in lactose. Owing to its many industrial applications, the biotechnological potential of this enzyme is substantial. This protein has been expressed in yeast and purified for crystallization trials. However, optimization of the best crystallization conditions yielded crystals with poor diffraction quality that precluded further structural studies. Finally, the crystal quality was improved using the streak-seeding technique and a complete diffraction data set was collected at 2.8 Å resolution. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301483 Wed, 24 Feb 2010 00:00:00 +0100 3301483 http://www.medworm.com/index.php?rid=3301482&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5207 Community-acquired respiratory distress syndrome toxin (CARDS TX) is a 591-amino-acid protein with ADP-ribosyltransferase and vacuolating activities that damages the cells lining the respiratory tracts of patients infected with the bacterial pathogen Mycoplasma pneumoniae. Crystals of CARDS TX were grown in space group C2, with unit-cell parameters a = 191.4, b = 107.4, c = 222.1 Å, β = 90.6°. A complete 2.2 Å data set was obtained from a single CARDS TX crystal. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301482 Wed, 24 Feb 2010 00:00:00 +0100 3301482 http://www.medworm.com/index.php?rid=3301481&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fub5003 Dichelobacter nodosus is the principal causative agent of ovine footrot, a disease of significant economic importance to the sheep industry. D. nodosus secretes a number of subtilisin-like serine proteases which mediate tissue damage and presumably contribute to the pathogenesis of footrot. Strains causing virulent footrot secrete the proteases AprV2, AprV5 and BprV and strains causing benign footrot secrete the closely related proteases AprB2, AprB5 and BprB. Here, the cloning, purification and crystallization of AprV2, AprB2, BprV and BprB are reported. Crystals of AprV2 and AprB2 diffracted to 2.0 and 1.7 Å resolution, respectively. The crystals of both proteases belonged to space group P1, with unit-cell parameters a = 43.1, b = 46.0, c = 47.2 Å, α = 97.8, β = 115.2, γ = 11... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301481 Wed, 24 Feb 2010 00:00:00 +0100 3301481 http://www.medworm.com/index.php?rid=3301480&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5246 Streptococcus pneumoniae SP0987, which was identified as a hypothetical protein, has a very low sequence identity to other well characterized lysozyme structures. Since determination of three-dimensional structure is a powerful means of functional characterization, X-ray crystallography has been used to accomplish this task. Here, the expression, purification, crystallization and preliminary crystallographic analysis of SP0987 from Streptococcus pneumoniae TIGR4 are reported. The crystal belonged to space group P212121 (with unit-cell parameters a = 36.46, b = 40.89, c = 147.44 Å) and diffracted to a resolution of 1.85 Å. The crystals are most likely to contain one molecule in the asymmetric unit, with a VM value of 2.02 Å3 Da−1. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301480 Wed, 24 Feb 2010 00:00:00 +0100 3301480 http://www.medworm.com/index.php?rid=3301479&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fuo5002 A thermostable manganese(II)-dependent 2,3-dihydroxybiphenyl-1,2-dioxygenase derived from Bacillus sp. JF8 was crystallized. The initial screening for crystallization was performed by the sitting-drop vapour-diffusion method using a crystallization robot, resulting in the growth of two crystal forms. The first crystal belonged to space group P1, with unit-cell parameters a = 62.7, b = 71.4, c = 93.6 Å, α = 71.2, β = 81.0, γ = 64.0°, and diffracted to 1.3 Å resolution. The second crystal belonged to space group I222, with unit-cell parameters a = 74.2, b = 90.8, c = 104.3 Å, and diffracted to 1.3 Å resolution. Molecular-replacement trials using homoprotocatechuate 2,3-dioxygenase from Arthrobacter globiformis (28% amino-acid sequence identity) as a search model provided a s... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301479 Wed, 24 Feb 2010 00:00:00 +0100 3301479 http://www.medworm.com/index.php?rid=3301478&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fus5003 A novel diadenosine 5′,5′′′-P1,P4-tetraphosphate (Ap4A) phosphorylase (Rv2613c) from Mycobacterium tuberculosis H37Rv has been crystallized by the sitting-drop vapour-diffusion method. The crystal belonged to space group C2, with unit-cell parameters a = 101.5, b = 63.6, c = 79.1 Å, β = 110.9°. The diffraction of the crystals extended to 1.9 Å resolution. The asymmetric unit is expected to contain two molecules of Rv2613c, with a corresponding crystal volume per protein weight (VM) of 2.41 Å3 Da−1 and a solvent content of 49.1%. This is the first report of a crystal of Ap4A phosphorylase. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301478 Wed, 24 Feb 2010 00:00:00 +0100 3301478 http://www.medworm.com/index.php?rid=3301477&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5281 Cyanide-insensitive alternative oxidase (AOX) is a mitochondrial membrane protein and a non-proton-pumping ubiquinol oxidase that catalyzes the four-electron reduction of dioxygen to water. In the African trypanosomes, trypanosome alternative oxidase (TAO) functions as a cytochrome-independent terminal oxidase that is essential for survival in the mammalian host; hence, the enzyme is considered to be a promising drug target for the treatment of trypanosomiasis. In the present study, recombinant TAO (rTAO) overexpressed in haem-deficient Escherichia coli was purified and crystallized at 293 K by the hanging-drop vapour-diffusion method using polyethylene glycol 400 as a precipitant. X-ray diffraction data were collected at 100 K and were processed to 2.9 Å resolution with 93.1% com... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301477 Wed, 24 Feb 2010 00:00:00 +0100 3301477 http://www.medworm.com/index.php?rid=3301476&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbo5071 MaoC-like dehydratase (MaoC) plays an important role in supplying (R)-3-hydroxyacyl-CoA from the fatty-acid oxidation pathway to polyhydroxyalkanoate (PHA) biosynthetic pathways. PHAs have been attracting much attention as they can be used in the biosynthesis of synthetic plastics. Crystals of MaoC from Phytophora capsici were grown by the hanging-drop vapour-diffusion method at 289 K in a number of screening conditions. An MaoC crystal diffracted to 1.93 Å resolution using X-ray radiation and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 81.458, b = 82.614, c = 124.228 Å, α = β = γ = 90°. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301476 Wed, 24 Feb 2010 00:00:00 +0100 3301476 http://www.medworm.com/index.php?rid=3301475&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fub5002 Bacteria of the Burkholderia cepacia complex (Bcc) have emerged as important opportunistic pathogens, establishing lung infections in immunocompromised or cystic fibrosis patients. Bcc uses polysaccharide-biofilm production in order to evade the host immune response. The biofilm precursor UDP-glucuronic acid is produced by a twofold NAD+-dependent oxidation of UDP-glucose. In B. cepacia IST408 this enzymatic reaction is performed by the UDP-glucose dehydrogenase BceC, a 470-residue enzyme, the production and crystallization of which are described here. The crystals belonged to the orthorhombic space group P212121 and contained four molecules in the asymmetric unit. Their crystallographic analysis at 2.09 Å resolution and a molecular-replacement study are reported. (Source: Acta Crysta... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301475 Wed, 24 Feb 2010 00:00:00 +0100 3301475 http://www.medworm.com/index.php?rid=3301474&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5272 Lucina pectinata haemoglobin II (HbII) transports oxygen in the presence of H2S to the symbiotic system in this bivalve mollusc. The composition of the haem pocket at the distal site includes TyrB10 and GlnE7, which are very common in other haem proteins. Obtaining crystals of oxyHbII at various pH values is required in order to elucidate the changes in the conformations of TyrB10 and GlnE7 and structural scenarios induced by changes in pH. Here, the growth of crystals of oxyHbII using the capillary counterdiffusion (CCD) technique at various pH values using a two-step protocol is reported. In the first step, a mini-screen was used to validate sodium formate as the best precipitating reagent for the growth of oxyHbII crystals. The second step, a pH screen typically used for optimization, ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3301474 Wed, 24 Feb 2010 00:00:00 +0100 3301474 http://www.medworm.com/index.php?rid=3297761&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5152 The inclusion of novel small molecules in crystallization experiments has provided very encouraging results and this method is now emerging as a promising alternative strategy for crystallizing `problematic' biological macromolecules. These small molecules have the ability to promote lattice formation through stabilizing intermolecular interactions in protein crystals. Here, the use of 1,3,6,8-pyrenetetrasulfonic acid (PTS), which provides a helpful intermolecular bridge between Leishmania mexicana PYK (LmPYK) macromolecules in the crystal, is reported, resulting in the rapid formation of a more stable crystal lattice at neutral pH and greatly improved X-ray diffraction results. The refined structure of the LmPYK–PTS complex revealed the negatively charged PTS molecule to be stacked betw... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297761 Tue, 23 Feb 2010 16:34:24 +0100 3297761 http://www.medworm.com/index.php?rid=3297770&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftt5016 Attempts to crystallize the noncovalent complex of recombinant human insulin with polysialic acid were carried out under normal and microgravity conditions. Both crystal types belonged to the same space group, I213, with unit-cell parameters a = b = c = 77.365 Å, α = β = γ = 90.00°. The reported space group and unit-cell parameters are almost identical to those of cubic insulin reported in the PDB. The results of X-ray studies confirmed that the crystals obtained were cubic insulin crystals and that they contained no polysialic acid or its fragments. Electron-density maps were calculated using X-ray diffraction sets from earth-grown and microgravity-grown crystals and the three-dimensional structure of the insulin molecule was determined and refined. The conformation and secondary-... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297770 Tue, 23 Feb 2010 00:00:00 +0100 3297770 http://www.medworm.com/index.php?rid=3297769&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5151 Fungal laccases are oxidoreductases that belong to the multinuclear copper-containing oxidases. They are able to oxidize a wide range of substrates, preferably phenolic compounds, which makes them suitable for employment in the bioremediation of soil and water as well as in other biotechnological applications. Here, the structural analysis of natural laccase B (LacB) from Trametes sp. AH28-2 is presented. This structure provides the opportunity to study the natural post-translational modifications of the enzyme. The overall fold shows a high homology to those of previously analyzed laccases with known three-dimensional structure. However, LacB contains a new structural element, a protruding loop near the substrate-binding site, compared with the previously reported laccase structures. T... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297769 Tue, 23 Feb 2010 00:00:00 +0100 3297769 http://www.medworm.com/index.php?rid=3297768&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftb5021 The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50 K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-reduction site, which consists of haem and a Cu atom (the haem a3–CuB site). Electron density for the NO molecule was observed close to CuB. The refined structure indicates that NO is bound to CuB in a side-on manner. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297768 Tue, 23 Feb 2010 00:00:00 +0100 3297768 http://www.medworm.com/index.php?rid=3297767&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5147 In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 Å resolution and in the molybdate-bound conformation at 2.25 and 2.45 Å resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed α/β domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the `Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacteria... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297767 Tue, 23 Feb 2010 00:00:00 +0100 3297767 http://www.medworm.com/index.php?rid=3297766&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fsw5033 4-Diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy-d-xylulose 5-phosphate or mevalonate-independent biosynthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and Gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C-methyl-d-erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C-methyl-d-ery... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297766 Tue, 23 Feb 2010 00:00:00 +0100 3297766 http://www.medworm.com/index.php?rid=3297765&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftb5017 In a subset of patients with the hereditary kidney-stone disease primary hyperoxaluria type 1 (PH1), the liver-specific enzyme alanine:glyoxylate aminotransferase (AGT) is mistargeted from peroxisomes to mitochondria. This is a consequence of the combined presence of the common P11L polymorphism and a disease-specific G170R mutation. In this paper, the crystal structure of mutant human AGT containing the G170R replacement determined at a resolution of 2.6 Å is reported. The crystal structure of AGT consists of an intimate dimer in which an extended N-terminal segment of 21 amino acids from one subunit wraps as an elongated irregular coil around the outside of the crystallographic symmetry-related subunit. In addition to the N-terminal segment, the monomer structure contains a large dom... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297765 Tue, 23 Feb 2010 00:00:00 +0100 3297765 http://www.medworm.com/index.php?rid=3297764&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5401 CNTO4088 is a monoclonal antibody to human IL-23. The X-ray structure of the Fab fragment revealed an unusual noncanonical conformation of CDR L1. Most antibodies with the κ light chain exhibit a canonical structure for CDR L1 in which residue 29 anchors the CDR loop to the framework. Analysis of the residues believed to define the conformation of CDR L1 did not explain why it should not adopt a canonical conformation in this antibody. This makes CNTO4088 a benchmark case for developing prediction methods and structure-modeling tools. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297764 Tue, 23 Feb 2010 00:00:00 +0100 3297764 http://www.medworm.com/index.php?rid=3297763&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftb5019 In addition to the common use of glutaraldehyde to nonspecifically cross-link protein crystals through lysine residues disposed on the surface of the protein, the use of gentle vapour diffusion of glutaraldehyde offers a convenient way to limit polymerization and to allow slow diffusion throughout the crystal. In the case of trimeric barnase crystals, a specific cross-link was observed between an lysine side chain and an arginine side chain that were spatially disposed at the ideal distance on the protein surface in the three monomers. Here, the direct observation of a specific Lys–Arg cross-link site is reported and a mechanism is proposed for the reaction. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297763 Tue, 23 Feb 2010 00:00:00 +0100 3297763 http://www.medworm.com/index.php?rid=3297762&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5154 The crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 Å resolution. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four-helix up–down–down–up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3297762 Tue, 23 Feb 2010 00:00:00 +0100 3297762 http://www.medworm.com/index.php?rid=3215740&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0416 (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215740 Thu, 28 Jan 2010 16:41:08 +0100 3215740 http://www.medworm.com/index.php?rid=3215760&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc9072 Additional funding is acknowledged by the authors of Hee et al. [Acta Cryst. (2009), F65, 422–425]. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215760 Thu, 28 Jan 2010 00:00:00 +0100 3215760 http://www.medworm.com/index.php?rid=3215759&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5405 Fas-associated factor 1 (FAF1) is a multifunctional pro-apoptotic protein that is involved in Fas-mediated apoptosis, NF-κB signalling and the ubiquitin–proteasome pathway. In the ubiquitin–proteasome pathway, FAF1 binds to the N domain of p97/VCP, a molecular chaperone that acts in complex with the proteasome, through its C-terminal UBX domain and inhibits the proteasomal protein-degradation process. In an effort to elucidate the structural basis of the function of FAF1 in modulating p97/VCP activity related to proteasomal protein degradation, crystallographic analysis of the FAF1 UBX domain and the p97/VCP N domain was initiated. Following the recently reported crystallization of the FAF1 UBX domain bound to the p97/VCP N domain, the unbound FAF1 UBX domain was also crystallized fo... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215759 Thu, 28 Jan 2010 00:00:00 +0100 3215759 http://www.medworm.com/index.php?rid=3215758&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5093 Transcription elongation by eukaryotic RNA polymerase II requires the coupling of mRNA synthesis and mRNA processing and export. The essential protein Iws1 is at the interface of these processes through its interaction with histone chaperone and elongation factor Spt6 as well as with complexes involved in mRNA processing and export. Upon crystallization of the evolutionarily conserved domain of Iws1 from Encephalitozoon cuniculi, four different crystal forms were obtained. Three of the crystal forms belonged to space group P21 and one belonged to space group P2221. Preliminary X-ray crystallographic analysis of one of the crystal forms allowed the collection of data to 2.5 Å resolution. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215758 Thu, 28 Jan 2010 00:00:00 +0100 3215758 http://www.medworm.com/index.php?rid=3215757&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5211 Psu, a coat protein from bacteriophage P4, inhibits Rho-dependent transcription termination both in vivo and in vitro. The Psu protein is α-helical in nature and appeared to be a dimer in solution. It interacts with Rho and affects the ATP binding and RNA-dependent ATPase activity of Rho, which in turn reduces the rate of RNA release from the elongation complex. Crystals of Psu were grown in space group I422 in the presence of PEG, with unit-cell parameters a = b = 148.76, c = 63.38 Å and a calculated Matthews coefficient of 2.1 Å3 Da−1 (41.5% solvent content), assuming the presence of two molecules in the asymmetric unit. A native data set was collected to 2.3 Å resolution. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215757 Thu, 28 Jan 2010 00:00:00 +0100 3215757 http://www.medworm.com/index.php?rid=3215756&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5324 VSP1 is a defence protein in Arabidopsis thaliana that may also be involved in control of plant development. The recombinant protein has been overexpressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method. The crystal diffracted to 1.9 Å resolution and a complete X-ray data set was collected at 100 K using Cu Kα radiation from a rotating-anode X-ray source. The crystals belonged to space group C2. As there are no related structures that could be used as a search model for molecular replacement, work is in progress on experimental phasing using heavy-atom derivatives and selenomethionine derivatives. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215756 Thu, 28 Jan 2010 00:00:00 +0100 3215756 http://www.medworm.com/index.php?rid=3215755&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fuo5003 In this study, the mature form of SPN48 was overexpressed in Escherichia coli and purified. The purified SPN48 protein was crystallized using 14% polyethylene glycol 8000 and 0.1 M 2-(N-morpholino)ethanesulfonic acid pH 6.0 as the precipitant. The crystals diffracted X-rays to 2.1 Å resolution and were suitable for structure determination. The crystals belonged to space group P21. The crystal structure will provide information regarding how SPN48 achieves its unusual specificity for its target protease. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215755 Thu, 28 Jan 2010 00:00:00 +0100 3215755 http://www.medworm.com/index.php?rid=3215754&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbo5069 Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein with a single SH2 domain that specifically binds to focal adhesion kinase (FAK) when residue Tyr925 of FAK is phosphorylated. The Grb2–FAK interaction is associated with cellular integrin-activated signal transduction events leading to the activation of the Ras-MAPK pathway. Crystals of the Grb2 SH2 domain in complex with a phosphopeptide corresponding to residues 921–930 of FAK have been obtained using the sitting-drop vapour-diffusion technique. The crystals belonged to space group P3121, with unit-cell parameters a = b = 102.7, c = 127.6 Å, α = β = 90.0, γ = 120.0°. A diffraction data set was collected from a flash-cooled crystal at 100 K to 2.49 Å resolution using synchrotron radiation. Structure dete... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215754 Thu, 28 Jan 2010 00:00:00 +0100 3215754 http://www.medworm.com/index.php?rid=3215753&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5096 The DEAD-box RNA helicase DDX5 is involved in many aspects of RNA processing and has been implicated in a number of cellular processes involving alteration of RNA secondary structure. The N-terminal region of DDX5, which contains the conserved domain 1 of the DEAD-box helicases, has been cloned and expressed in Escherichia coli and purified. Here, the crystallization and preliminary diffraction analysis of this region is reported. X-ray diffraction data were processed to a resolution of 2.7 Å. The crystals belonged to space group I222, with unit-cell parameters a = 66.18, b = 73.80, c = 104.00 Å, α = β = γ = 90°. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215753 Thu, 28 Jan 2010 00:00:00 +0100 3215753 http://www.medworm.com/index.php?rid=3215752&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbo5072 Glycine decarboxylase, or P-protein, is a major enzyme that is involved in the C1 metabolism of all organisms and in the photorespiratory pathway of plants and cyanobacteria. The protein from Synechocystis sp. PCC 6803 is a homodimer with a mass of 215 kDa. Recombinant glycine decarboxylase was expressed in Escherichia coli and purified by metal-affinity, ion-exchange and gel-filtration chromatography. Crystals of P-protein that diffracted to a resolution of 2.1 Å were obtained using the hanging-drop vapour-diffusion method at 291 K. X-ray diffraction data were collected from cryocooled crystals using synchrotron radiation. The crystals belonged to space group P212121, with unit-cell parameters a = 96.30, b = 135.81, c = 179.08 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215752 Thu, 28 Jan 2010 00:00:00 +0100 3215752 http://www.medworm.com/index.php?rid=3215751&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5048 1,3-Propanediol dehydrogenase is an enzyme that catalyzes the oxidation of 1,3-propanediol to 3-hydroxypropanal with the simultaneous reduction of NADP+ to NADPH. SeMet-labelled 1,3-propanediol dehydrogenase protein from the hyperthermophilic bacterium Aquifex aeolicus VF5 was overexpressed in Escherichia coli and purified to homogeneity. Crystals of this protein were grown from an acidic buffer with ammonium sulfate as the precipitant. Single-wavelength data were collected at the selenium peak to a resolution of 2.4 Å. The crystal belonged to space group P32, with unit-cell parameters a = b = 142.19, c = 123.34 Å. The structure contained two dimers in the asymmetric unit and was solved by the MR-SAD approach. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215751 Thu, 28 Jan 2010 00:00:00 +0100 3215751 http://www.medworm.com/index.php?rid=3215750&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5282 The study of proteins involved in de novo biosynthesis of purine nucleotides is central in the development of antibiotics and anticancer drugs. In view of this, a protein from the hyperthermophile Pyrococcus horikoshii OT3 was isolated, purified and crystallized using the microbatch method. Its primary structure was found to be similar to that of SAICAR synthetase, which catalyses the seventh step of de novo purine biosynthesis. A diffraction-quality crystal was obtained using Hampton Research Crystal Screen II condition No. 34, consisting of 0.05 M cadmium sulfate hydrate, 0.1 M HEPES buffer pH 7.5 and 1.0 M sodium acetate trihydrate, with 40%(v/v) 1,4-butanediol as an additive. The crystal belonged to space group P31, with unit-cell parameters a = b = 95.62, c = 149.13 Å. Ass... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215750 Thu, 28 Jan 2010 00:00:00 +0100 3215750 http://www.medworm.com/index.php?rid=3215749&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fub5004 The minor pilin FctB is an integral part of the pilus assembly expressed by Streptococcus pyogenes. Since it is located at the cell wall, it can be hypothesized that it functions as a cell-wall anchor for the streptococcal pilus. In order to elucidate its structure, the genes for FctB from the S. pyogenes strains 90/306S and SF370 were cloned for overexpression in Escherichia coli. FctB from strain 90/306S was crystallized by the sitting-drop vapour-diffusion method using sodium citrate as a precipitant. The hexagonal FctB crystals belonged to space group P61 or P65, with unit-cell parameters a = b = 95.15, c = 100.25 Å, and diffracted to 2.9 Å resolution. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215749 Thu, 28 Jan 2010 00:00:00 +0100 3215749 http://www.medworm.com/index.php?rid=3215748&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5400 Human hookworms are among the most pathogenic soil-transmitted helminths. These parasitic nematodes have co-evolved with the host and are able to maintain a high worm burden for decades without killing the human host. However, it is possible to develop vaccines against laboratory-challenge hookworm infections using either irradiated third-state infective larvae (L3) or enzymes from the adult parasites. In an effort to control hookworm infection globally, the Human Hookworm Vaccine Initiative, a product-development partnership with the Sabin Vaccine Institute to develop new control tools including vaccines, has identified a battery of protein antigens, including surface-associated antigens (SAAs) from L3. SAA proteins are characterized by a 13 kDa conserved domain of unknown function. SAA... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215748 Wed, 27 Jan 2010 00:00:00 +0100 3215748 http://www.medworm.com/index.php?rid=3215747&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5325 The antitoxin Phd from the phd/doc module of bacteriophage P1 was crystallized in two distinct crystal forms. Crystals of His-tagged Phd contain a C-terminally truncated version of the protein and diffract to 2.20 Å resolution. Crystals of untagged Phd purified from the Phd–Doc complex diffract to 2.25 Å resolution. These crystals are partially merohedrally twinned and contain the full-length version of the protein. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215747 Wed, 27 Jan 2010 00:00:00 +0100 3215747 http://www.medworm.com/index.php?rid=3215746&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5320 The opium poppy Papaver somniferum is the source of the narcotic analgesics morphine and codeine. Salutaridine reductase (SalR; EC 1.1.1.248) reduces the C-7 keto group of salutaridine to the C-7 (S)-hydroxyl group of salutaridinol in the biosynthetic pathway that leads to morphine in the opium poppy plant. P. somniferum SalR was overproduced in Escherichia coli and purified using cobalt-affinity and size-exclusion chromatography. Hexagonal crystals belonging to space group P6422 or P6222 were obtained using ammonium sulfate as precipitant and diffracted to a resolution of 1.9 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215746 Wed, 27 Jan 2010 00:00:00 +0100 3215746 http://www.medworm.com/index.php?rid=3215745&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5089 In this study, GmhB has been cloned, expressed, purified and crystallized. X-ray data have also been collected to 2.50 Å resolution using synchrotron radiation. The crystal belonged to space group P6, with unit-cell parameters a = 243.2, b = 243.2, c = 41.1 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215745 Wed, 27 Jan 2010 00:00:00 +0100 3215745 http://www.medworm.com/index.php?rid=3215744&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5002 RspB is a surface adhesin of Erysipelothrix rhusiopathiae. A recombinant form of the collagen-binding region of this protein, RspB(31–348), has been overexpressed in Escherichia coli in native and selenomethionine-derivative forms and purified using affinity and gel-permeation chromatography. Thin plate-like crystals were obtained by the hanging-drop vapour-diffusion method using the same condition for both forms. The native crystals diffracted to a resolution of 2.5 Å using an in-house X-ray source, while the selenomethionine-derivative crystals diffracted to a resolution of 2.2 Å using synchrotron radiation. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 46.19, b = 66.65, c = 101.72 Å, β = 94.11°. (Source: Acta Crystallographica Secti... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215744 Wed, 27 Jan 2010 00:00:00 +0100 3215744 http://www.medworm.com/index.php?rid=3215743&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5397 The 1.6 Å resolution structure of the micromolar competitive inhibitor S-(N,N-dimethylaminoethyl) phenylacetothiohydroximate-O-sulfate bound to Sinapis alba myrosinase, a plant thioglucosidase, is reported. Myrosinase and its substrates, the glucosinolates, are part of the plant's defence system. The sulfate group and the phenyl group of the inhibitor bind to the aglycon-binding site of the enzyme, whereas the N,N-dimethyl group binds to the glucose-binding site and explains the large improvement in binding affinity compared with previous compounds. The structure suggests ways to increase the potency and specificity of the compound by improving the interactions with the hydrophobic pocket of the aglycon-binding site. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215743 Wed, 27 Jan 2010 00:00:00 +0100 3215743 http://www.medworm.com/index.php?rid=3215742&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5244 The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKα2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in respons... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215742 Wed, 27 Jan 2010 00:00:00 +0100 3215742 http://www.medworm.com/index.php?rid=3215741&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fsw5034 Copper amine oxidases (CAOs) are ubiquitous in nature and catalyse the oxidative deamination of primary amines to the corresponding aldehydes. Humans have three viable CAO genes (AOC1–3). AOC1 encodes human diamine oxidase (hDAO), which is the frontline enzyme for histamine metabolism. hDAO is unique among CAOs in that it has a distinct substrate preference for diamines. The structure of hDAO in space group P212121 with two molecules in the asymmetric unit has recently been reported. Here, the structure of hDAO refined to 2.1 Å resolution in space group C2221 with one molecule in the asymmetric unit is reported. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3215741 Wed, 27 Jan 2010 00:00:00 +0100 3215741 http://www.medworm.com/index.php?rid=3207796&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5017 Bovine pancreatic ribonuclease A (RNase A) was crystallized from a mixture of small molecules containing basic fuchsin, tobramycin and uridine 5′-monophosphate (U5P). Solution of the crystal structure revealed that the enzyme was selectively bound to U5P, with the pyrimidine ring of U5P residing in the pyrimidine-binding site at Thr45. The structure was refined to an R factor of 0.197 and an Rfree of 0.253. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3207796 Tue, 26 Jan 2010 16:18:23 +0100 3207796 http://www.medworm.com/index.php?rid=3207798&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftb5012 The crystal structure of Vibrio cholerae uracil-DNA N-glycosylase (vcUNG) has been determined to 1.5 Å resolution. Based on this structure, a homology model of Aliivibrio salmonicida uracil-DNA N-glycosylase (asUNG) was built. A previous study demonstrated that asUNG possesses typical cold-adapted features compared with vcUNG, such as a higher catalytic efficiency owing to increased substrate affinity. Specific amino-acid substitutions in asUNG were suggested to be responsible for the increased substrate affinity and the elevated catalytic efficiency by increasing the positive surface charge in the DNA-binding region. The temperature adaptation of these enzymes has been investigated using structural and mutational analyses, in which mutations of vcUNG demonstrated an increased substrat... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3207798 Tue, 26 Jan 2010 00:00:00 +0100 3207798 http://www.medworm.com/index.php?rid=3207797&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5137 The crystal structure of Bacillus amyloliquefaciens α-amylase (BAA) at 1.4 Å resolution revealed ambiguities in the thermal adaptation of homologous proteins in this family. The final model of BAA is composed of two molecules in a back-to-back orientation, which is likely to be a consequence of crystal packing. Despite a high degree of identity, comparison of the structure of BAA with those of other liquefying-type α-amylases indicated moderate discrepancies at the secondary-structural level. Moreover, a domain-displacement survey using anisotropic B-factor and domain-motion analyses implied a significant contribution of domain B to the total flexibility of BAA, while visual inspection of the structure superimposed with that of B. licheniformis α-amylase (BLA) indicated higher flexi... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3207797 Tue, 26 Jan 2010 00:00:00 +0100 3207797 http://www.medworm.com/index.php?rid=3120068&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0410 (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120068 Fri, 25 Dec 2009 15:41:43 +0100 3120068 http://www.medworm.com/index.php?rid=3120096&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fme0399 (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120096 Fri, 25 Dec 2009 00:00:00 +0100 3120096 http://www.medworm.com/index.php?rid=3120095&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5075 Inositol 1,3,4,5,6-pentakisphosphate kinase (IP5 2-K) is an enzyme involved in inositol metabolism that synthesizes IP6 (inositol 1,2,3,4,5,6-hexakisphosphate) from inositol 1,3,4,5,6-pentakisphosphate (IP5) and ATP. IP6 is the major phosphorus reserve in plants, while in mammals it is involved in multiple cellular events such as DNA editing and chromatin remodelling. In addition, IP6 is the precursor of other highly phosphorylated inositols which also play highly relevant roles. IP5 2-K is the only enzyme that phosphorylates the 2-OH axial position of the inositide and understanding its molecular mechanism of substrate specificity is of great interest in cell biology. IP5 2-K from Arabidopsis thaliana has been expressed in Escherichia coli as two different fusion proteins and purified. B... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120095 Fri, 25 Dec 2009 00:00:00 +0100 3120095 http://www.medworm.com/index.php?rid=3120094&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5394 In order to understand the biological properties of the immune systems of waterfowl and to establish a system for structural studies of duck class I major histocompatibility complex (DuMHC I), a complex of DuMHC I with duck β2-microglobulin (Duβ2m) and the peptide AEIEDLIF (AF8) derived from H5N1 NP residues 251–258 was assembled. The complex was crystallized; the crystals belonged to space group C2221, with unit-cell parameters a = 54.7, b = 72.4, c = 102.2 Å, and diffracted to 2.3 Å resolution. Matthews coefficient calculation and initial structure determination by molecular replacement showed that the crystals did not contain the whole DuMHC I complex, but instead contained the DuMHC I α3 domain and a Duβ2m molecule (DuMHC I α3+β2m). Another complex of DuMHC I with the... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120094 Fri, 25 Dec 2009 00:00:00 +0100 3120094 http://www.medworm.com/index.php?rid=3120093&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5390 F-box proteins are the substrate-recognition components of Skp1–Cullin1–F-box protein–Rbx1 (SCF) ubiquitin ligase complexes. Fbs1, an F-box protein, binds specifically to proteins modified with high-mannose oligosaccharides. Fbg3, another F-box protein, has 51% sequence identity to Fbs1. Although the residues that are necessary for binding to oligosaccharides are conserved between Fbs1 and Fbg3, Fbg3 does not bind glycoproteins. Skp1 and Fbg3 were co-expressed in Escherichia coli and their complex was purified to homogeneity and crystallized. Microseeding combined with the sandwiched hanging-drop technique improved the quality of the resulting crystals. The plate-shaped crystals belonged to space group P212121, with unit-cell parameters a = 34.1, b = 76.6, c = 193.9 Å and one mo... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120093 Fri, 25 Dec 2009 00:00:00 +0100 3120093 http://www.medworm.com/index.php?rid=3120092&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5045 The measles virus (MV) hemagglutinin (MV-H) mediates the attachment of MV particles to cell-surface receptors for entry into host cells. MV uses two receptors for attachment to host cells: the complement-control protein CD46 and the signalling lymphocyte activation molecule (SLAM). The MV-H glycoprotein from an Edmonston MV variant and the MV-binding fragment of the CD46 receptor were overproduced in mammalian cells and used to crystallize an MV-H–CD46 complex. Well diffracting crystals containing two complexes in the asymmetric unit were obtained and the structure of the complex was solved by the molecular-replacement method. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120092 Fri, 25 Dec 2009 00:00:00 +0100 3120092 http://www.medworm.com/index.php?rid=3120091&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5243 Shewanella oneidensis is an environmentally versatile Gram-negative γ-proteobacterium that is endowed with an unusually large proteome of redox proteins. Of the four old yellow enzyme (OYE) homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group P212121 and were moderately pseudo-merohedrally twinned, emulating a P422 metric symmetry. The native crystals of SYE4 were of exceptional diffraction quality and provided complete data to 1.10 Å resolution using synchrotron radiation, while crystals of the reduced enzyme and of the enzyme in complex with a wide ra... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120091 Fri, 25 Dec 2009 00:00:00 +0100 3120091 http://www.medworm.com/index.php?rid=3120090&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5326 The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, althoug... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120090 Fri, 25 Dec 2009 00:00:00 +0100 3120090 http://www.medworm.com/index.php?rid=3120089&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5094 Eukaryotic ribonucleases P and MRP are closely related RNA-based enzymes which contain a catalytic RNA component and several protein subunits. The roles of the protein subunits in the structure and function of eukaryotic ribonucleases P and MRP are not clear. Crystals of a complex that included a circularly permuted 46-nucleotide-long P3 domain of the RNA component of Saccharomyces cerevisiae ribonuclease MRP and selenomethionine derivatives of the shared ribonuclease P/MRP protein components Pop6 (18.2 kDa) and Pop7 (15.8 kDa) were obtained using the sitting-drop vapour-diffusion method. The crystals belonged to space group P4222 (unit-cell parameters a = b = 127.2, c = 76.8 Å, α = β = γ = 90°) and diffracted to 3.25 Å resolution. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120089 Fri, 25 Dec 2009 00:00:00 +0100 3120089 http://www.medworm.com/index.php?rid=3120088&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5090 PACSIN 1, which is mainly detected in brain tissue, is one of the PACSIN-family proteins involved in endocytosis and recruitment of synaptic vesicles. It binds to dynamin, synaptojanin 1 and N-WASP, and functions in vesicle formation and transport. However, the mechanisms of action of PACSIN 1 in these processes are largely unknown. Here, full-length and five C-terminal truncation constructs of human PACSIN 1 have been successfully expressed and purified in Escherichia coli. PACSIN 1 (1–344) was crystallized and diffracted to a resolution of 3.0 Å. The crystal belonged to space group C2, with unit-cell parameters a = 158.65, b = 87.38, c = 91.76 Å, α = 90.00, β = 113.61, γ = 90.00°. There were two molecules in the asymmetric unit and the solvent content was estimated to be ab... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120088 Fri, 25 Dec 2009 00:00:00 +0100 3120088 http://www.medworm.com/index.php?rid=3120087&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5076 Gellan gum, a commercial gelling agent produced by Sphingomonas elodea ATCC 31461, is a high-value microbial exopolysaccharide. UDP-glucose dehydrogenase (UGD; EC 1.1.1.22) is responsible for the NAD-dependent twofold oxidation of UDP-glucose to UDP-glucuronic acid, one of the key components for gellan biosynthesis. S. elodea ATCC 31461 UGD, termed UgdG, was cloned, expressed, purified and crystallized in native and SeMet-derivatized forms in hexagonal and tetragonal space groups, respectively; the crystals diffracted X-rays to 2.40 and 3.40 Å resolution, respectively. Experimental phases were obtained for the tetragonal SeMet-derivatized crystal form by a single-wavelength anomalous dispersion experiment. This structure was successfully used as a molecular-replacement probe for the he... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120087 Fri, 25 Dec 2009 00:00:00 +0100 3120087 http://www.medworm.com/index.php?rid=3120086&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5391 RNA polymerase (RNAP) elongates RNA by iterative nucleotide-addition cycles (NAC). A specific structural state (or states) of RNAP may be the target of transcription elongation factors. Gfh1, a Thermus thermophilus Gre-family protein, inhibits NAC. To elucidate which RNAP structural state Gfh1 associates with, the T. thermophilus RNAP elongation complex (EC) was cocrystallized with Gfh1. Of the 70 DNA/RNA scaffolds tested, two (for EC1 and EC2) were successfully crystallized. In the presence of Gfh1, EC1 and EC2 yielded crystals belonging to space group P21 with similar unit-cell parameters (crystals 1 and 2, respectively). X-ray diffraction data sets were obtained at 3.6 and 3.8 Å resolution, respectively. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120086 Fri, 25 Dec 2009 00:00:00 +0100 3120086 http://www.medworm.com/index.php?rid=3120085&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5049 Human interferon-λ1 (IFN-λ1Ins) and the extracellular domain of interferon-λ1 receptor (IFN-λ1R1) were expressed in Drosophila S2 cells and purified to homogeneity. Both IFN-λ1Ins and interferon-λ1 produced from Escherichia coli (IFN-λ1Bac) were coupled with IFN-λ1R1 at room temperature and the complexes were purified by gel filtration. Both complexes were crystallized; the crystals were flash-frozen at 100 K and diffraction data were collected to 2.16 and 2.1 Å, respectively. Although the IFN-λ1Bac–IFN-λ1R1 and IFN-λ1Ins–IFN-λ1R1 complexes differed only in the nature of the expression system used for the ligand, their crystallization conditions and crystal forms were quite different. A search for heavy-atom derivatives as well as molecular-replacement trials are in pr... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120085 Fri, 25 Dec 2009 00:00:00 +0100 3120085 http://www.medworm.com/index.php?rid=3120084&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5072 Dihydrodipicolinate reductase (DHDPR; EC 1.3.1.26) catalyzes the nucleotide (NADH/NADPH) dependent second step of the lysine-biosynthesis pathway in bacteria and plants. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPR from methicillin-resistant Staphylococcus aureus (MRSA-DHDPR) are presented. The enzyme was crystallized in a number of forms, predominantly with ammonium sulfate as a precipitant, with the best crystal form diffracting to beyond 3.65 Å resolution. Crystal structures of the apo form as well as of cofactor (NADPH) bound and inhibitor (2,6-pyridinedicarboxylate) bound forms of MRSA-DHDPR will provide insight into the structure and function of this essential enzyme and valid drug target. (Source: Acta Crystallog... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120084 Fri, 25 Dec 2009 00:00:00 +0100 3120084 http://www.medworm.com/index.php?rid=3120083&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5205 Lon is an oligomeric ATP-dependent protease that degrades defective or denatured proteins as well as some folded proteins for the control of cellular protein quality and metabolism. Lon from Thermococcus onnurineus NA1 was purified and crystallized at 295 K. A 2.0 Å resolution data set was collected using synchrotron radiation. The crystals belonged to space group P63, with unit-cell parameters a = 121.45, b = 121.45, c = 195.24 Å. Assuming the presence of two monomers in the asymmetric unit, the solvent content was estimated to be about 60.7%. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120083 Fri, 25 Dec 2009 00:00:00 +0100 3120083 http://www.medworm.com/index.php?rid=3120082&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5393 Ribosome-inactivating proteins (RIPs) inhibit protein synthesis and induce cell death by removing a single adenine from a specific rRNA loop. They can be divided into two main groups: type 1 and type 2 RIPs. Type 1 RIPs are single-chain enzymes with N-glycosidase activity. Type 2 RIPs contain two chains (A and B) linked by a disulfide bond. The A chain has RIP enzymatic activity, whereas the B chain shows lectin activity and is able to bind to glycosylated receptors on the cell surface. Stenodactylin is a type 2 RIP from the caudex of Adenia stenodactyla from the Passifloraceae family that has been recently purified and characterized. It shows a strong enzymatic activity towards several substrates and is more cytotoxic than other toxins of the same type. Here, the crystallization and preli... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120082 Fri, 25 Dec 2009 00:00:00 +0100 3120082 http://www.medworm.com/index.php?rid=3120081&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5241 In this study, the N-terminal fragment of the GyrB subunit of DNA gyrase from Xanthomonas oryzae pv. oryzae was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 2.10 Å resolution using a synchrotron-radiation source. The crystal belonged to space group I41, with unit-cell parameters a = b = 110.27, c = 70.75 Å. The asymmetric unit contained one molecule, with a VM of 2.57 Å3 Da−1 and a solvent content of 50.2%. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120081 Fri, 25 Dec 2009 00:00:00 +0100 3120081 http://www.medworm.com/index.php?rid=3120080&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5050 Saccharomyces cerevisiae α-galactosidase is a highly glycosylated extracellular protein that catalyzes the hydrolysis of α-galactosidic linkages in various glucids. Its enzymatic activity is of interest in many food-related industries and has biotechnological applications. Glycosylated and in vitro deglycosylated protein samples were both assayed for crystallization, but only the latter gave good-quality crystals that were suitable for X-ray crystallography. The crystals belonged to space group P4212, with unit-cell parameters a = b = 101.24, c = 111.52 Å. A complete diffraction data set was collected to 1.95 Å resolution using a synchrotron source. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120080 Fri, 25 Dec 2009 00:00:00 +0100 3120080 http://www.medworm.com/index.php?rid=3120079&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5043 p97/VCP is a multifunctional AAA+-family ATPase that is involved in diverse cellular processes. p97/VCP directly interacts with various adaptors for activity in different biochemical contexts. Among these adaptors are p47 and Fas-associated factor 1 (FAF1), which contain a common UBX domain through which they bind to the N domain of p97/VCP. In the ubiquitin–proteasome pathway, p97/VCP acts as a chaperone that presents client proteins to the proteasome for degradation, while FAF1 modulates the process by interacting with ubiquitinated client proteins and also with p97/VCP. In an effort to elucidate the structural details of the interaction between p97/VCP and FAF1, the p97/VCP N domain was crystallized in complex with the FAF1 UBX domain. X-ray data were collected to 2.60 Å resolution... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120079 Fri, 25 Dec 2009 00:00:00 +0100 3120079 http://www.medworm.com/index.php?rid=3120078&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5045 Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P41212 and diffracted to 2.0 Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6 Å. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial Rfree of 0.456 and Rwork of 0.416. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120078 Fri, 25 Dec 2009 00:00:00 +0100 3120078 http://www.medworm.com/index.php?rid=3120077&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5234 Dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) catalyzes the rate-limiting step in the (S)-lysine biosynthesis pathway of bacteria and plants. Here, the cloning of the DHDPS gene from a clinical isolate of Streptococcus pneumoniae (OXC141 strain) and the strategy used to express, purify and crystallize the recombinant enzyme are described. Diffracting crystals were grown in high-molecular-weight PEG precipitants using the hanging-drop vapour-diffusion method. The best crystal, from which data were collected, diffracted to beyond 2.0 Å resolution. Initially, the crystals were thought to belong to space group P42212, with unit-cell parameters a = 105.5, b = 105.5, c = 62.4 Å. However, the R factors remained high following initial processing of the data. It was subsequently shown tha... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120077 Fri, 25 Dec 2009 00:00:00 +0100 3120077 http://www.medworm.com/index.php?rid=3120076&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5191 The human C-type lectin-like protein CLEC5A (also known as MDL-1) is expressed on the surface of myeloid cells and plays a critical role in dengue-virus-induced disease by signalling through the transmembrane adaptor protein DAP12. The C-type lectin-like domain of CLEC5A was expressed in Escherichia coli, refolded and purified. Recombinant CLEC5A crystals were grown by sitting-drop vapour diffusion using polyethylene glycol 6000 as a precipitant. After optimization, crystals were grown which diffracted to 1.56 Å using synchrotron radiation. The results presented in this paper suggest that crystals producing diffraction of this quality will be suitable for structural determination of human CLEC5A. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120076 Fri, 25 Dec 2009 00:00:00 +0100 3120076 http://www.medworm.com/index.php?rid=3120075&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5210 The opportunistic pathogen Pseudomonas aeruginosa secretes a protein that triggers the accelerated degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells. This protein, which is known as the CFTR inhibitory factor (Cif), acts as a virulence factor and may facilitate airway colonization by P. aeruginosa. Based on sequence similarity Cif appears to be an epoxide hydrolase (EH), but it lacks several of the conserved features found in the active sites of canonical members of the EH family. Here, the crystallization of purified recombinant Cif by vapor diffusion is reported. The crystals formed in space group C2, with unit-cell parameters a = 167.4, b = 83.6, c = 88.3 Å, β = 100.6°. The crystals diffracted to 2.39 Å resolution on a rot... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120075 Fri, 25 Dec 2009 00:00:00 +0100 3120075 http://www.medworm.com/index.php?rid=3120074&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5395 NADH:rubredoxin oxidoreductase (NROR), an O2-inducible protein, is a versatile electron donor for scavengers of O2 and reactive oxygen species (ROS) in Clostridium acetobutylicum. Recombinant NROR was overexpressed in Escherichia coli and purified to homogeneity; it was subsequently crystallized using the sitting-drop vapour-diffusion method at 293 K. Preliminary crystallographic analysis revealed that the crystals belonged to space group P4122 or P4322, with unit-cell parameters a = b = 98.6, c = 88.3 Å, and diffracted to 2.1 Å resolution. Assuming that the crystals contained one molecule per asymmetric unit, the Matthews coefficient was calculated to be 2.7 Å3 Da−1 and the solvent content to be 54.1%. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120074 Fri, 25 Dec 2009 00:00:00 +0100 3120074 http://www.medworm.com/index.php?rid=3120073&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5005 Malonyl-CoA:acyl-carrier protein transacylase (MCAT), encoded by the fabd gene, is a key enzyme in type II fatty-acid biosynthesis. It is responsible for transferring the malonyl group from malonyl-CoA to the holo acyl-carrier protein (ACP). Since the type II system differs from the type I system that mammals use, it has received enormous attention as a possible antibiotic target. In particular, only a single isoform of MCAT has been reported and a continuous coupled enzyme assay has been developed. MCAT from Staphylococcus aureus was overexpressed in Escherichia coli and the protein was purified and crystallized. Diffraction data were collected to 1.2 Å resolution. The crystals belonged to space group P21, with unit-cell parameters a = 41.608, b = 86.717, c = 43.163 Å, α = γ = 9... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120073 Fri, 25 Dec 2009 00:00:00 +0100 3120073 http://www.medworm.com/index.php?rid=3120072&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5238 Death-associated protein 5 (DAP5) is a member of the eIF4G family of scaffolding proteins that mediate cap-independent translation initiation by recruiting the translational machinery to internal ribosomal entry sites (IRESs) on mRNA. The MIF4G domain of DAP5 directly interacts with the eukaryotic initiation factors eIF4A and eIF3 and enhances the translation of several viral and cellular IRESs. Here, the crystallization and preliminary X-ray diffraction analysis of the MIF4G domain of DAP5 is presented. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120072 Fri, 25 Dec 2009 00:00:00 +0100 3120072 http://www.medworm.com/index.php?rid=3120071&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5312 The stromal-cell-derived factor 2-like protein of Arabidopsis thaliana (AtSDL) has been shown to be highly up-regulated in response to unfolded protein response (UPR) inducing reagents, suggesting that it plays a crucial role in the plant UPR pathway. AtSDL has been cloned, overexpressed, purified and crystallized using the vapour-diffusion method. Two crystal forms have been obtained under very similar conditions. The needle-shaped crystals did not diffract X-rays, while the other form diffracted to 1.95 Å resolution using a synchrotron-radiation source and belonged to the hexagonal space group P61, with unit-cell parameters a = b = 96.1, c = 69.3 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120071 Fri, 25 Dec 2009 00:00:00 +0100 3120071 http://www.medworm.com/index.php?rid=3120070&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftt5017 The crystal structure of the hypothetical protein YqgQ from Bacillus subtilis has been determined to 2.1 Å resolution. The crystals belonged to space group P21, with unit-cell parameters a = 51.85, b = 41.25, c = 55.18 Å, β = 113.4°, and contained three protein molecules in the asymmetric unit. The structure was determined by the single-wavelength anomalous dispersion method using selenium-labeled protein and was refined to a final R factor of 24.7% (Rfree = 28.0%). The protein molecule mainly comprises a three-helical bundle. Its putative function is inferred to be single-stranded nucleic acid binding based on sequence and structural homology. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120070 Fri, 25 Dec 2009 00:00:00 +0100 3120070 http://www.medworm.com/index.php?rid=3120069&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fkw5016 Azoreductase 1 from Pseudomonas aeruginosa strain PAO1 (paAzoR1) catalyses the activation of the prodrug balsalazide and reduces the azo dye methyl red using reduced nicotinamide adenine dinucleotide cofactor as an electron donor. To investigate the mechanism of the enzyme, a Y131F mutation was introduced and the enzymic properties of the mutant were compared with those of the wild-type enzyme. The crystallographic structure of the mutant with methyl red bound was solved at 2.1 Å resolution and compared with the wild-type structure. Tyr131 is important in the architecture of the active site but is not essential for enzymic activity. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3120069 Fri, 25 Dec 2009 00:00:00 +0100 3120069 http://www.medworm.com/index.php?rid=3070517&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5116 The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3070517 Tue, 08 Dec 2009 00:00:00 +0100 3070517 http://www.medworm.com/index.php?rid=3070516&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fwd5117 The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the `open' conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the `closed' structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic sur... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3070516 Tue, 08 Dec 2009 00:00:00 +0100 3070516 http://www.medworm.com/index.php?rid=3035759&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5140 The structure of a probable Mo-cofactor biosynthesis protein B from Sulfolobus tokodaii, belonging to space group P6422 with unit-cell parameters a = b = 136.68, c = 210.52 Å, was solved by molecular replacement to a resolution of 1.9 Å and refined to an R factor and Rfree of 16.8% and 18.5%, respectively. The asymmetric unit contains a trimer, while the biologically significant oligomer is predicted to be a hexamer by size-exclusion chromatography. The subunit structure and fold of ST2315 are similar to those of other enzymes that are known to be involved in the molybdopterin- and molybdenum cofactor-biosynthesis pathways. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035759 Sat, 28 Nov 2009 15:49:06 +0100 3035759 http://www.medworm.com/index.php?rid=3035787&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5396 The DNA-repair enzyme endonuclease IV from the thermophilic bacterium Thermotoga maritima MSB8 (reference sequence NC_000853) has been expressed in Escherichia coli and crystallized for X-ray analysis. T. maritima endonuclease IV is a 287-amino-acid protein with 32% sequence identity to E. coli endonuclease IV. The protein was purified to homogeneity and was crystallized using the sitting-drop vapor-diffusion method. The protein crystallized in space group P61, with one biological molecule in the asymmetric unit, corresponding to a Matthews coefficient of 2.39 Å3 Da−1 and 47% solvent content. The unit-cell parameters of the crystals were a = b = 123.2, c = 35.6 Å. Microseeding and further optimization yielded crystals with an X-ray diffraction limit of 2.36 Å. A single 70° d... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035787 Fri, 27 Nov 2009 00:00:00 +0100 3035787 http://www.medworm.com/index.php?rid=3035786&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fus5002 Maleylacetate reductase (EC 1.3.1.32) is an important enzyme that is involved in the degradation pathway of aromatic compounds and catalyzes the reduction of maleylacetate to 3-oxoadipate. The gene pnpD encoding maleylacetate reductase in Burkholderia sp. strain SJ98 was cloned, expressed in Escherichia coli and purified by affinity chromatography. The enzyme was crystallized in both native and SeMet-derivative forms by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant at 293 K. The crystals belonged to space group P21212, with unit-cell parameters a = 72.91, b = 85.94, c = 53.07 Å. X-ray diffraction data for the native and SeMet-derivative crystal were collected to 2.7 and 2.9 Å resolution, respectively. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035786 Fri, 27 Nov 2009 00:00:00 +0100 3035786 http://www.medworm.com/index.php?rid=3035785&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fub5001 The condensation of ammonium and glutamate into glutamine catalyzed by glutamine synthetase (GS) is a fundamental step in nitrogen metabolism in all kingdoms of life. In plants, this is preceded by the reduction of inorganic nitrogen to an ammonium ion and therefore effectively articulates nitrogen fixation and metabolism. Although the three-dimensional structure of the dodecameric bacterial GS was determined quite some time ago, the quaternary architecture of the plant enzyme has long been assumed to be octameric, mostly on the basis of low-resolution electron-microscopy studies. Recently, the crystallographic structure of a monocotyledonous plant GS was reported that revealed a homodecameric organization. In order to unambiguously establish the quaternary architecture of GS from dicotyle... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035785 Fri, 27 Nov 2009 00:00:00 +0100 3035785 http://www.medworm.com/index.php?rid=3035784&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fus5001 Russell's viper venom blood coagulation factor V activator (RVV-V) is a thrombin-like serine proteinase that specifically activates factor V by cleaving a single peptide bond between Arg1545 and Ser1546. Activated factor V combines with activated factor X produced by the enzyme RVV-X in the venom to form the prothombinase complex, which can induce disseminated intravascular coagulopathy in envenomated animals. In the current study, RVV-V was crystallized in order to attempt to understand its substrate specificity for factor V. Four distinct crystal forms of RVV-V were obtained using the sitting-drop vapour-diffusion method and diffraction data sets were collected on SPring-8 beamlines. The best crystal of RVV-V generated data sets to 1.9 Å resolution. (Source: Acta Crystallographica S... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035784 Fri, 27 Nov 2009 00:00:00 +0100 3035784 http://www.medworm.com/index.php?rid=3035783&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5239 REV7 is involved in various cellular functions including DNA replication, signal transduction and cell-cycle regulation. In DNA replication, REV7 interacts with REV3 and forms DNA polymerase ζ, which plays a central role in error-prone DNA synthesis. REV3 is a catalytic subunit and its activity is stimulated by REV7. To clarify the structural basis of the interaction between REV7 and REV3, human REV7 was crystallized in complex with a REV3 fragment. Two crystal forms were obtained. Crystal forms I and II belonged to space groups P21, with unit-cell parameters a = 43.8, b = 50.0, c = 107.3 Å, β = 96.9°, and P41212 or P43212, with unit-cell parameters a = b = 76.6, c = 118.4 Å, respectively. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035783 Fri, 27 Nov 2009 00:00:00 +0100 3035783 http://www.medworm.com/index.php?rid=3035782&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5006 Many agarolytic bacteria degrade agar polysaccharide into the disaccharide unit neoagarobiose [O-3,6-anhydro-α-l-galactopyranosyl-(1→3)-d-galactose] using various β-agarases. Neoagarobiose hydrolase is an enzyme that acts on the α-1,3 linkage in neoagarobiose to yield d-galactose and 3,6-anhydro-l-galactose. This activity is essential in both the metabolism of agar by agarolytic bacteria and the production of fermentable sugars from agar biomass for bioenergy production. Neoagarobiose hydrolase from the marine bacterium Saccharophagus degradans 2-40 was overexpressed in Escherichia coli and crystallized in the monoclinic space group C2, with unit-cell parameters a = 129.83, b = 76.81, c = 90.11 Å, β = 101.86°. The crystals diffracted to 1.98 Å resolution and possibly contain... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035782 Fri, 27 Nov 2009 00:00:00 +0100 3035782 http://www.medworm.com/index.php?rid=3035781&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5277 Hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea is a homotrimeric protein that catalyzes the oxidation of hydroxylamine to nitrite. Each monomer, with a molecular weight of 67.1 kDa, contains seven c-type hemes and one heme P460, the porphyrin ring of which is covalently linked to a tyrosine residue from an adjacent subunit. HAO was first crystallized and structurally characterized at a resolution of 2.8 Å in 1997. The structure was solved in space group P63 and suffered from merohedral twinning. Here, a crystallization procedure is presented that yielded untwinned crystals belonging to space group P21212, which diffracted to 2.25 Å resolution and contained one trimer in the asymmetric unit. The unit-cell parameters were a = 140.7, b = 142.6, c = 107.4 Å. (Source... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035781 Fri, 27 Nov 2009 00:00:00 +0100 3035781 http://www.medworm.com/index.php?rid=3035780&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5046 Monomeric Azami-Green (mAG) from the stony coral Galaxea fascicularis is the first monomeric green-emitting fluorescent protein that is not a derivative of Aequorea victoria green fluorescent protein (avGFP). mAG and avGFP are 27% identical in amino-acid sequence. Diffraction-quality crystals of recombinant mAG were obtained by the sitting-drop vapour-diffusion method using PEG 3350 as the precipitant. The mAG crystal diffracted X-rays to 2.20 Å resolution on beamline AR-NW12A at the Photon Factory (Tsukuba, Japan). The crystal belonged to space group P1, with unit-cell parameters a = 41.78, b = 51.72, c = 52.89 Å, α = 90.96, β = 103.41, γ = 101.79°. The Matthews coefficient (VM = 2.10 Å3 Da−1) indicated that the crystal contained two mAG molecules per asymmetric unit.... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035780 Fri, 27 Nov 2009 00:00:00 +0100 3035780 http://www.medworm.com/index.php?rid=3035779&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5231 The punA gene of the cariogenic pathogen Streptococcus mutans encodes purine nucleoside phosphorylase (PNP), which is a pivotal enzyme in the nucleotide-salvage pathway, catalyzing the phosphorolysis of purine nucleosides to generate purine bases and α-ribose 1-phosphate. In the present work, the PNP protein was expressed in Escherichia coli strain BL21 (DE3) in a soluble form at a high level. After purification of the PNP enzyme, the protein was crystallized using the sitting-drop vapour-diffusion technique; the crystals diffracted to 1.6 Å resolution at best. The crystals belonged to space group H3, with unit-cell parameters a = b = 113.0, c = 60.1 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035779 Fri, 27 Nov 2009 00:00:00 +0100 3035779 http://www.medworm.com/index.php?rid=3035778&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5276 FAD synthetase from Corynebacterium ammoniagenes (CaFADS), a prokaryotic bifunctional enzyme that catalyses the phosphorylation of riboflavin as well as the adenylylation of FMN, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. Diffraction-quality cubic crystals of native and selenomethionine-labelled (SeMet-CaFADS) protein belonged to the cubic space group P213, with unit-cell parameters a = b = c = 133.47 Å and a = b = c = 133.40 Å, respectively. Data sets for native and SeMet-containing crystals were collected to 1.95 and 2.42 Å resolution, respectively. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035778 Fri, 27 Nov 2009 00:00:00 +0100 3035778 http://www.medworm.com/index.php?rid=3035777&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5047 In this study, the purified stoPCNA2–stoPCNA3 complex was crystallized by hanging-drop vapour diffusion. The crystals obtained belonged to the orthorhombic space groups I222 and P21212, with unit-cell parameters a = 91.1, b = 111.8, c = 170.9 Å and a = 91.1, b = 160.6, c = 116.6 Å, respectively. X-ray diffraction data sets were collected to 2.90 Å resolution for the I222 crystals and to 2.80 Å resolution for the P21212 crystals. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035777 Fri, 27 Nov 2009 00:00:00 +0100 3035777 http://www.medworm.com/index.php?rid=3035776&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5206 Small heat-shock proteins (sHsps) are ubiquitous molecular chaperones. sHsps function as homooligomers or heterooligomers that are prone to subunit exchange and structural plasticity. Here, a procedure for obtaining diffraction-quality crystals of the α-crystallin domain of human Hsp27 is presented. Initially, limited proteolysis was used to delineate the corresponding stable fragment (residues 90–171). This fragment could be crystallized, but examination of the crystals using X-rays indicated partial disorder. The surface-entropy reduction approach was applied to ameliorate the crystal quality. Consequently, a double mutant E125A/E126A of the 90–171 fragment yielded well ordered crystals that diffracted to 2.0 Å resolution. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035776 Fri, 27 Nov 2009 00:00:00 +0100 3035776 http://www.medworm.com/index.php?rid=3035775&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5319 Exo-β-1,3-galactanase from Phanerochaete chrysosporium (Pc1,3Gal43A) consists of a glycoside hydrolase family 43 catalytic domain and a substrate-binding domain that belongs to carbohydrate-binding module family 35. It catalyzes the hydrolysis of β-1,3-galactan, which is the backbone of the arabinogalactan proteins; the C-terminal carbohydrate-binding module family 35 domain increases the local concentration of the enzyme around β-1,3-galactan by its high affinity for the substrate. To enable phase determination using the multiwavelength anomalous dispersion method, selenomethionyl Pc1,3Gal43A was crystallized at 298 K using the hanging-drop vapour-diffusion method. The presence of selenium in the crystals was confirmed from the X-ray absorption spectrum. The crystals belonged to spa... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035775 Fri, 27 Nov 2009 00:00:00 +0100 3035775 http://www.medworm.com/index.php?rid=3035774&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5074 Modification (HsdM) and specificity (HsdS) subunits are constituents of an active methyltransferase (MTase) of multifunctional type I restriction enzymes. To provide a molecular background on HsdM, a putative hsdM gene from Vibrio vulnificus YJ016 (HsdM_Vv) was cloned and the expressed protein was purified and crystallized from 22%(w/v) polyethylene glycol 8000, 0.02 M imidazole pH 7.5 and 5 mM β-mercaptoethanol. Diffraction data were collected to 1.86 Å resolution using synchrotron radiation. The crystal belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 78.9, c = 165.8 Å. With one molecule in the asymmetric unit, the crystal volume per unit protein weight was 2.12 Å3 Da−1, with a solvent content of 42%. (Source: Acta Crystallogra... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035774 Fri, 27 Nov 2009 00:00:00 +0100 3035774 http://www.medworm.com/index.php?rid=3035773&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5204 A 16 kDa buckwheat protein (BWp16) is a major allergen responsible for immediate hypersensitivity reactions including anaphylaxis. A deletion mutant of BWp16 (rBWp16ΔN) was overproduced and purified and was shown to be immunologically active. A three-wavelength MAD data set was collected from a crystal of selenomethionine-labelled rBWp16ΔN. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 28.39, b = 31.54, c = 32.20 Å, α = 111.92, β = 108.91, γ = 98.74°. One monomer was expected to be present in the asymmetric unit based on the calculated Matthews coefficient of 1.76 Å3 Da−1. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035773 Fri, 27 Nov 2009 00:00:00 +0100 3035773 http://www.medworm.com/index.php?rid=3035772&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5073 SIGN-R1, or CD209b, is a mouse C-type lectin receptor that is expressed at high levels on macrophages in lymphoid tissues, especially within the marginal zone of the spleen. SIGN-R1 can bind and mediate the uptake of various microbial polysaccharides, including dextrans, lipopolysaccharides and pneumococcal capsular polysaccharides. It has been shown that SIGN-R1 mediates the clearance of encapsulated pneumococcus, complement fixation via binding C1q independent of antibody and innate resistance to pneumococcal infection. Recently, SIGN-R1 has also been demonstrated to bind sialylated antibody and mediate its activity to suppress autoimmunity. The carbohydrate-recognition domain (CRD) of SIGN-R1 has been cloned and overexpressed in a soluble secretory form in mammalian Chinese hamster ovar... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035772 Fri, 27 Nov 2009 00:00:00 +0100 3035772 http://www.medworm.com/index.php?rid=3035771&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5071 Ets proteins are transcription factors that activate or repress the expression of genes that are involved in various biological processes, including cellular proliferation, differentiation, development, transformation and apoptosis. Like other Ets-family members, Elf3 functions as a sequence-specific DNA-binding transcriptional factor. A mouse Elf3 C-terminal fragment (amino-acid residues 269–371) containing the DNA-binding domain has been crystallized in complex with mouse type II TGF-β receptor promoter (TβR-II) DNA. The crystals belonged to space group P212121, with unit-cell parameters a = 42.66, b = 52, c = 99.78 Å, and diffracted to a resolution of 2.2 Å. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035771 Fri, 27 Nov 2009 00:00:00 +0100 3035771 http://www.medworm.com/index.php?rid=3035770&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5240 The structure of the extracellular domain of human CD69 has been determined by single-crystal X-ray diffraction. The structure refined to 1.37 Å resolution provides further details of the overall structure and the asymmetric interface between the monomers in the native dimer. The protein was crystallized using di[poly(ethylene glycol)] adipate, which also served as a cryoprotectant. This is the first report of a crystal structure determined using crystals grown with this polymer. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035770 Fri, 27 Nov 2009 00:00:00 +0100 3035770 http://www.medworm.com/index.php?rid=3035769&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fsw5032 The crystal structure of the PDZ1 domain of human PSD-93 has been determined to 2.0 Å resolution. The PDZ1 domain forms a crystallographic trimer that is also predicted to be stable in solution. The main contributions to the stabilization of the trimer seem to arise from interactions involving the PDZ1–PDZ2 linker region at the extreme C-terminus of PDZ1, implying that the oligomerization that is observed is not of biological significance in full-length PSD-93. Comparison of the structures of the binding cleft of PSD-93 PDZ1 with the previously reported structures of PSD-93 PDZ2 and PDZ3 as well as of the closely related human PSD-95 PDZ1 shows that they are very similar in terms of amino-acid composition. However, the cleft is significantly narrower in PSD-95. This could be part of t... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035769 Fri, 27 Nov 2009 00:00:00 +0100 3035769 http://www.medworm.com/index.php?rid=3035768&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ftb5014 Glycolate oxidase, a peroxisomal flavoenzyme, generates glyoxylate at the expense of oxygen. When the normal metabolism of glyoxylate is impaired by the mutations that are responsible for the genetic diseases hyperoxaluria types 1 and 2, glyoxylate yields oxalate, which forms insoluble calcium deposits, particularly in the kidneys. Glycolate oxidase could thus be an interesting therapeutic target. The crystal structure of human glycolate oxidase (hGOX) in complex with 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole (CCPST) has been determined at 2.8 Å resolution. The inhibitor heteroatoms interact with five active-site residues that have been implicated in catalysis in homologous flavodehydrogenases of l-2-hydroxy acids. In addition, the chlorophenyl substituent is surrounded ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035768 Fri, 27 Nov 2009 00:00:00 +0100 3035768 http://www.medworm.com/index.php?rid=3035767&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgx5150 In prokaryotic organisms, cold shock triggers the production of a small highly conserved family of cold-shock proteins (CSPs). CSPs have been well studied structurally and functionally in Escherichia coli and Bacillus subtilis, but Salmonella typhimurium CSPs remain relatively uncharacterized. In S. typhimurium, six homologous CSPs have been identified: StCspA–E and StCspH. The crystal structure of cold-shock protein E from S. typhimurium (StCspE) has been determined at 1.1 Å resolution and has an R factor of 0.203 after refinement. The three-dimensional structure is similar to those of previously determined CSPs and is composed of five antiparallel β-strands forming a classic OB fold/five-stranded β-barrel. This first structure of a CSP from S. typhimurium provides new insight into... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035767 Fri, 27 Nov 2009 00:00:00 +0100 3035767 http://www.medworm.com/index.php?rid=3035766&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5145 The pyridoxal 5′-phosphate-dependent enzyme 4-amino-4-deoxychorismate lyase converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate in one of the crucial steps in the folate-biosynthesis pathway. The primary structure of the hypothetical protein TTHA0621 from Thermus thermophilus HB8 suggests that TTHA0621 is a putative 4-amino-4-deoxychorismate lyase. Here, the crystal structure of TTHA0621 is reported at 1.93 Å resolution. The asymmetric unit contained four NCS molecules related by 222 noncrystallographic symmetry, in which the formation of intact dimers may be functionally important. The cofactor pyridoxal 5′-phosphate (PLP) binds to the protein in the large cleft formed by the N-terminal and C-terminal domains of TTHA0621. The high structural similarity and the conser... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035766 Fri, 27 Nov 2009 00:00:00 +0100 3035766 http://www.medworm.com/index.php?rid=3035765&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5144 The X-ray crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj-GAPDH) was determined to 1.81 Å resolution. The crystal belonged to space group C2221, with unit-cell parameters a = 83.4, b = 152.0, c = 118.6 Å. The structure was solved by molecular replacement and was refined to a final R factor of 17.1% (Rfree = 19.8%). The final structure included the cofactor NADP+ at the nucleotide-binding site and featured unoccupied inorganic and substrate phosphate-binding sites. A comparison with GAPDH structures from mesophilic sources suggested that Mj-GAPDH is stabilized by extensive electrostatic interactions between the C-terminal α-helices and various distal loop regions, which are likely to contrib... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035765 Fri, 27 Nov 2009 00:00:00 +0100 3035765 http://www.medworm.com/index.php?rid=3035764&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5146 In bacteria and plants, dihydrodipicolinate synthase (DHDPS) plays a key role in the (S)-lysine biosynthesis pathway. DHDPS catalyzes the first step of the condensation of (S)-aspartate-β-semialdehyde and pyruvate to form an unstable compound, (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. The activity of DHDPS is allosterically regulated by (S)-lysine, a feedback inhibitor. The crystal structure of DHDPS from Methanocaldococcus jannaschii (MjDHDPS) was solved by the molecular-replacement method and was refined to 2.2 Å resolution. The structure revealed that MjDHDPS forms a functional homotetramer, as also observed in Escherichia coli DHDPS, Thermotoga maritima DHDPS and Bacillus anthracis DHDPS. The binding-site region of MjDHDPS is essentially similar to those found in oth... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035764 Fri, 27 Nov 2009 00:00:00 +0100 3035764 http://www.medworm.com/index.php?rid=3035763&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5142 The structure of TM1254, a putative β-phosphoglucomutase from T. maritima, was determined to 1.74 Å resolution in a high-throughput structural genomics programme. Diffraction data were obtained from crystals belonging to space group P22121, with unit-cell parameters a = 48.16, b = 66.70, c = 83.80 Å, and were refined to an R factor of 19.2%. The asymmetric unit contained one protein molecule which is comprised of two domains. Structural homologues were found from protein databases that confirmed a strong resemblance between TM1254 and members of the haloacid dehalogenase (HAD) hydrolase family. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035763 Fri, 27 Nov 2009 00:00:00 +0100 3035763 http://www.medworm.com/index.php?rid=3035762&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5141 Ribose-5-phosphate isomerase is a ubiquitous intracellular enzyme of bacterial, plant and animal origin that is involved in the pentose phosphate cycle, an essential component of cellular carbohydrate metabolism. Specifically, the enzyme catalyses the reversible conversion of ribose 5-phosphate to ribulose 5-phosphate. The structure of ribose-5-phosphate isomerase from Methanocaldococcus jannaschii has been solved in space group P21 to 1.78 Å resolution using molecular replacement with one homotetramer in the asymmetric unit and refined to an R factor of 14.8%. The active site in each subunit was occupied by two molecules of propylene glycol in different orientations, one of which corresponds to the location of the phosphate moiety and the other to the location of the furanose ring of ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035762 Fri, 27 Nov 2009 00:00:00 +0100 3035762 http://www.medworm.com/index.php?rid=3035761&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5139 The crystal structure of d-lactate dehydrogenase from Aquifex aeolicus (aq_727) was determined to 2.12 Å resolution in space group P212121, with unit-cell parameters a = 90.94, b = 94.43, c = 188.85 Å. The structure was solved by molecular replacement using the coenzyme-binding domain of Lactobacillus helveticus d-lactate dehydrogenase and contained two homodimers in the asymmetric unit. Each subunit of the homodimer was found to be in a `closed' conformation with the NADH cofactor bound to the coenzyme-binding domain and with a lactate (or pyruvate) molecule bound at the interdomain active-site cleft. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035761 Fri, 27 Nov 2009 00:00:00 +0100 3035761 http://www.medworm.com/index.php?rid=3035760&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhv5143 SurE is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. The structure of the SurE protein from the hyperthermophile Aquifex aeolicus has been solved at 1.5 Å resolution using molecular replacement with one dimer in the asymmetric unit and refined to an R factor of 15.6%. The crystal packing reveals that two dimers assemble to form a tetramer, although gel-filtration chromatography showed the presence of only a dimer in solution. The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=3035760 Fri, 27 Nov 2009 00:00:00 +0100 3035760 http://www.medworm.com/index.php?rid=2946530&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fpu5279 γ-Carboxymucolactone decarboxylase (γ-CMD; EC 4.1.1.44) catalyzes the conversion of γ-carboxymucolactone to β-ketoadipate enol-lactone in the β-ketoadipate pathway, which is a key part of the degradation process of aromatic compounds in bacteria and in some eukaryotes such as fungi and yeast. γ-CMD from the thermophilic archaeon Sulfolobus solfataricus (Ss γ-CMD) is encoded by the pcaC gene and is composed of 139 amino-acid residues with a molecular mass of 15 945 Da. Ss γ-CMD was crystallized and X-ray data were collected to 2.40 Å resolution. The crystal belonged to space group P43212, with unit-cell parameters a = b = 66.66, c = 184.82 Å. The Matthews coefficient and solvent content were estimated to be 2.14 Å3 Da−1 and 42.6%, respectively, assuming that the asy... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946530 Fri, 30 Oct 2009 00:00:00 +0100 2946530 http://www.medworm.com/index.php?rid=2946529&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5092 An archaeal-type phosphoenolpyruvate carboxylase (PepcA) from Clostridium perfringens has been expressed in Escherichia coli in a soluble form with an amino-terminal His tag. The recombinant protein is enzymatically active and two crystal forms have been obtained. Complete diffraction data extending to 3.13 Å resolution have been measured from a crystal soaked in KAu(CN)2, using radiation at a wavelength just above the Au LIII edge. The asymmetric unit contains two tetramers of PepcA. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946529 Fri, 30 Oct 2009 00:00:00 +0100 2946529 http://www.medworm.com/index.php?rid=2946528&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5208 The intracellular β-glucosidase from Kluyveromyces marxianus NBRC1777 (KmBglI) belongs to glycoside hydrolase family 3 and has a unique domain architecture. Selenomethionine-labelled KmBglI was purified and crystallized by the hanging-drop vapour-diffusion method using the purified enzyme at 30 mg ml−1, 0.04 M potassium dihydrogen phosphate pH 5.1, 16%(w/v) PEG 8000 and 20%(v/v) glycerol. The crystal belonged to space group C2, with unit-cell parameters a = 245.8, b = 148.7, c = 119.9 Å, β = 112.9°. Multiple-wavelength anomalous dispersion data were collected at 2.4 and 2.5 Å resolution. A tetramer was assumed to be present in the asymmetric unit, which gave a Matthews coefficient of 2.6 Å3 Da−1. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946528 Fri, 30 Oct 2009 00:00:00 +0100 2946528 http://www.medworm.com/index.php?rid=2946527&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5044 PASTA subunits (∼70 amino acids) are specific to bacterial serine/threonine kinases and to penicillin-binding proteins (PBPs) and are involved in the synthesis of peptidoglycan. The human pathogen Staphylococcus aureus contains a serine/threonine kinase, Stk1, which plays a major role in virulence. A recombinant His-tagged portion of the extracellular domain of Stk1 containing three PASTA subunits has been crystallized using zinc sulfate as a crystallizing agent. The crystals belonged to the tetragonal space group P4122, with unit-cell parameters a = 68.0, b = 68.0, c = 158.1 Å. Structure determination by the MAD method is now in progress. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946527 Fri, 30 Oct 2009 00:00:00 +0100 2946527 http://www.medworm.com/index.php?rid=2946526&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5042 Mycobacterium tuberculosis DNA gyrase, a nanomachine that is involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target for fluoroquinolone action. The breakage-reunion domain of the A subunit plays an essential role in DNA binding during the catalytic cycle. Two constructs of 53 and 57 kDa (termed GA53BK and GA57BK) corresponding to this domain have been overproduced, purified and crystallized. Diffraction data were collected from four crystal forms. The resolution limits ranged from 4.6 to 2.7 Å depending on the crystal form. The best diffracting crystals belonged to space group C2, with a biological dimer in the asymmetric unit. This is the first report of the crystallization and preliminary X-ray diffraction... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946526 Fri, 30 Oct 2009 00:00:00 +0100 2946526 http://www.medworm.com/index.php?rid=2946525&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5237 The complex of Tamarindus indica Kunitz-type trypsin inhibitor and porcine trypsin has been crystallized by the sitting-drop vapour-diffusion method using ammonium acetate as precipitant and sodium acetate as buffer. The homogeneity of complex formation was checked by size-exclusion chromatography and further confirmed by reducing SDS–PAGE. The crystals diffracted to 2.0 Å resolution and belonged to the tetragonal space group P41, with unit-cell parameters a = b = 57.1, c = 120.1 Å. Preliminary X-ray diffraction analysis indicated the presence of one unit of inhibitor–trypsin complex per asymmetric unit, with a solvent content of 45%. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946525 Fri, 30 Oct 2009 00:00:00 +0100 2946525 http://www.medworm.com/index.php?rid=2946524&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fbw5316 Trypanosoma cruzi dihydrofolate reductase-thymidylate synthase (TcDHFR-TS) was crystallized in complexes with the dihydrotriazine-based or quinazoline-based antifolates C-448, cycloguanil (CYC) and Q-8 in order to gain insight into the interactions of this DHFR enzyme with classical and novel inhibitors. The TcDHFR-TS–C-448–NDP–dUMP crystal belonged to space group C2221 with two molecules per asymmetric unit and diffracted to 2.37 Å resolution. The TcDHFR-TS–CYC, TcDHFR-TS–CYC–NDP and TcDHFR-TS–Q-8–NDP crystals belonged to space group P21 with four molecules per asymmetric unit and diffracted to 2.1, 2.6 and 2.8 Å resolution, respectively. Crystals belonging to the two different space groups were suitable for structure determination. (Source: Acta Crystallographica Se... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946524 Fri, 30 Oct 2009 00:00:00 +0100 2946524 http://www.medworm.com/index.php?rid=2946523&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5236 Gallate dioxygenase (DesB) from Sphingobium sp. SYK-6, which belongs to the type II extradiol dioxygenase family, was purified and crystallized using the hanging-drop vapour-diffusion method. Two crystal forms were obtained. The form I crystal belonged to space group C2, with unit-cell parameters a = 136.2, b = 53.6, c = 55.1 Å, β = 112.8°, and diffracted to 1.6 Å resolution. The form II crystal belonged to space group P21, with unit-cell parameters a = 56.2, b = 64.7, c = 116.1 Å, β = 95.1°, and diffracted to 1.9 Å resolution. A molecular-replacement calculation using LigAB as a search model yielded a satisfactory solution for both crystal forms. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946523 Fri, 30 Oct 2009 00:00:00 +0100 2946523 http://www.medworm.com/index.php?rid=2946522&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5380 The human type II AAA+ protein p97 participates in various cellular activities, presumably through its involvement in the ubiquitin–proteasome degradation pathway. Mutations in p97 have been implicated in patients with inclusion-body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). In this work, three mutant p97 N-D1 fragments, R86A, R95G and R155H, were crystallized in the presence of ATPγS with PEG 3350 as a main precipitant, yielding two different crystal forms. The R155H mutant crystal belonged to space group R3, with unit-cell parameters in the hexagonal setting of a = b = 134.2, c = 182.9 Å, and was merohedrally twinned, with an estimated twin fraction of 0.34. The crystals of the R86A and R95G mutants belonged to space group P1, with s... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946522 Fri, 30 Oct 2009 00:00:00 +0100 2946522 http://www.medworm.com/index.php?rid=2946521&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5043 Schwanniomyces occidentalis invertase is an extracellular enzyme that releases β-fructose from the nonreducing termini of various β-d-fructofuranoside substrates. Its ability to produce 6-kestose by transglycosylation makes this enzyme an interesting research target for applications in industrial biotechnology. The enzyme has been expressed in Saccharomyces cerevisiae. Recombinant and wild-type forms, which showed different glycosylation patterns, were crystallized by vapour-diffusion methods. Although crystallization trials were conducted on both forms of the protein, crystals suitable for X-ray crystallographic analyses were only obtained from the wild-type enzyme. The crystals belonged to space group P212121, with unit-cell parameters a = 105.78, b = 119.49, c = 137.68 Å. A d... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946521 Fri, 30 Oct 2009 00:00:00 +0100 2946521 http://www.medworm.com/index.php?rid=2946520&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fxb5003 The T-cell response to human cytomegalovirus is characterized by a dramatic reduction of clonal diversity in patients undergoing chronic inflammation or immunodepression. In order to check whether all the selected high-avidity T-cell clones recognize the immunodominant pp65 peptide antigen pp65495–503 (NLVPMVATV) presented by the major histocompatibility complex (MHC) molecule HLA-A2 in a similar manner, several public high-affinity T-cell receptors (TCRs) specific for the pp65495–503–HLA-A2 complex have been investigated. Expression, purification and crystallization were performed and preliminary crystallographic data were collected to 4.7 Å resolution for the RA15 TCR in complex with the pp65495–503–HLA-A2 complex. Comparison of the RA15–pp65495–503–HLA-A2 complex mole... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946520 Fri, 30 Oct 2009 00:00:00 +0100 2946520 http://www.medworm.com/index.php?rid=2946519&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fnj5044 Escherichia coli isocitrate dehydrogenase (ICDH) can be phosphorylated and dephosphorylated by a single bifunctional protein, isocitrate dehydrogenase kinase/phosphatase (AceK), which is encoded by the aceK gene. In order to investigate the regulatory mechanism of (de)phosphorylation of ICDH by AceK, AceK was successfully cocrystallized in complex with its intact protein substrate, ICDH, in the presence of ATP. The complex crystal was obtained by the hanging-drop vapour-diffusion technique using PEG 300 as a precipitant and magnesium sulfate as an additive. SDS–PAGE analysis of dissolved crystals showed that the crystals contained both AceK and ICDH proteins. The complex crystals diffracted to a resolution of 2.9 Å in space group P63, with unit-cell parameters a = b = 196.80, c = 156... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946519 Fri, 30 Oct 2009 00:00:00 +0100 2946519 http://www.medworm.com/index.php?rid=2946518&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5203 The porcine adenovirus NADC-1 isolate, a strain of porcine adenovirus type 4, has a fibre with an atypical architecture. In addition to a classical virus-attachment region, shaft and head domains, it contains an additional galectin-like domain C-terminal to the head domain and connected to the head domain by a long RGD-containing loop. The galectin-like domain contains two putative carbohydrate-recognition domains. The head and galectin-like domains have been independently crystallized. Diffraction data have been obtained to 3.2 Å resolution from crystals of the head domain and to 1.9 Å resolution from galectin-like domain crystals. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946518 Fri, 30 Oct 2009 00:00:00 +0100 2946518 http://www.medworm.com/index.php?rid=2946517&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5200 Conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708 is a member of the NADPH-dependent aldo-keto reductase (AKR) superfamily and catalyzes the stereospecific reduction of ketopantoyl lactone to d-pantoyl lactone. A diffraction-quality crystal of recombinant CPR-C2 was obtained by the sitting-drop vapour-diffusion method using PEG 3350 as the precipitant. The crystal diffracted X-rays to 1.7 Å resolution on beamline NW12A of the Photon Factory-Advanced Ring (Tsukuba, Japan). The crystal belonged to space group P212121, with unit-cell parameters a = 55.02, b = 68.30, c = 68.93 Å. The Matthews coefficient (VM = 1.76 Å3 Da−1) indicated that the crystal contained one CPR-C2 molecule per asymmetric unit. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946517 Fri, 30 Oct 2009 00:00:00 +0100 2946517 http://www.medworm.com/index.php?rid=2946516&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5201 Rare sugars are used for many industrial and medical purposes and are produced by the interconversion between aldoses and ketoses catalyzed by sugar and sugar-phosphate isomerases. Recently, Clostridium thermocellum d-ribose-5-phosphate isomerase (CTRPI), an aldose–ketose isomerase, was cloned in order to synthesize d-allose and its substrate specificity was further characterized for industrial usage. CTRPI has a novel substrate specificity that differs from those of other isomerases, which have broad substrate specificities. CTRPI prefers aldose substrates such as l-talose, d-ribose and d-allose. CTRPI was purified and crystallized in order to determine its three-dimensional structure and thus to elucidate its enzymatic reaction mechanism and understand its substrate specificity. The cr... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946516 Fri, 30 Oct 2009 00:00:00 +0100 2946516 http://www.medworm.com/index.php?rid=2946515&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5070 In this report, a series of mutations at this crystal contact designed to both reduce side-chain entropy and replace the solvent-mediated interface with direct side-chain contacts are reported. The results suggest that improved crystal growth is achieved upon the introduction of direct crystal contacts, while little improvement is observed with side-chain entropy-reducing mutations alone. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946515 Fri, 30 Oct 2009 00:00:00 +0100 2946515 http://www.medworm.com/index.php?rid=2946514&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Frp5041 Proliferating cell nuclear antigen (PCNA) is a DNA-clamping protein that is responsible for increasing the processivity of the replicative polymerases during DNA replication and repair. The PCNA from the eurypsychrophilic archaeon Methanococcoides burtonii DSM 6242 (MbPCNA) has been targeted for protein structural studies. A recombinant expression system has been created that overproduces MbPCNA with an N-terminal hexahistidine affinity tag in Escherichia coli. As a result, recombinant MbPCNA with a molecular mass of 28.3 kDa has been purified to at least 95% homogeneity and crystallized by vapor-diffusion equilibration. Preliminary X-ray analysis revealed a trigonal hexagonal R3 space group, with unit-cell parameters a = b = 102.5, c = 97.5 Å. A single MbPCNA crystal was subjected to... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946514 Fri, 30 Oct 2009 00:00:00 +0100 2946514 http://www.medworm.com/index.php?rid=2946513&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fhc5087 RsbX from Bacillus subtilis is a manganese-dependent PPM phosphatase and negatively regulates the signal transduction of the general stress response by the dephosphorylation of RsbS and RsbR, which are activators of the alternative RNA polymerase σ factor SigB. In order to elucidate the structural–functional relationship of its Ser/Thr protein-phosphorylation mechanism, an X-ray crystallographic diffraction study of RsbX was performed. Recombinant RsbX was expressed in Escherichia coli, purified and crystallized. Crystals were obtained using the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 1.06 Å resolution with an Rmerge of 8.1%. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 33.3, b = 41.7, c = 68.6 Å, ... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946513 Fri, 30 Oct 2009 00:00:00 +0100 2946513 http://www.medworm.com/index.php?rid=2946512&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5388 AmtR, a member of the TetR family of transcription regulators, is a global regulator of nitrogen control in Corynebacterium glutamicum. Unlike other TetR-family members, which are regulated by small-molecule effectors, AmtR is regulated by a protein called GlnK. It has been shown that a GlnK trimer has to become adenylylated prior to formation of a complex with AmtR. The physiological function of AmtR has been very well studied, but structural characterization of the mechanistic aspects of AmtR-regulated transcription has yet to be accomplished. AmtR has successfully been crystallized in space group P21212, with six molecules in the asymmetric unit and unit-cell parameters a = 153.34, b = 163.10, c = 51.93 Å. Preliminary phases were obtained using Se-SAD. (Source: Acta Crystallograph... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946512 Fri, 30 Oct 2009 00:00:00 +0100 2946512 http://www.medworm.com/index.php?rid=2946511&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Ffw5232 Free methionine-(R)-sulfoxide reductase (fRMsr) catalyzes the reduction of the free form of methionine-(R)-sulfoxide back to free methionine. The fRMsr protein from Staphylococcus aureus was overexpressed in Escherichia coli, purified and crystallized at 295 K using ammonium sulfate as a precipitant. Diffraction data were collected to 1.7 Å resolution from a native crystal using synchrotron radiation. The crystal belonged to the hexagonal space group P6122, with unit-cell parameters a = b = 89.84, c = 88.75 Å, α = β = 90, γ = 120°. Assuming the presence of one molecule in the asymmetric unit, the calculated Matthews coefficient value was 2.21 Å3 Da−1, with a solvent content of 57.1%. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946511 Fri, 30 Oct 2009 00:00:00 +0100 2946511 http://www.medworm.com/index.php?rid=2946510&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5389 Nucleoside diphosphate kinases (NDKs; EC 2.7.4.6) play an essential role in the synthesis of nucleotides from intermediates in the salvage pathway in all parasitic trypanosomatids and their structural studies will be instrumental in shedding light on the biochemical machinery involved in the parasite life cycle and host–parasite interactions. In this work, NDKb from Leishmania major was overexpressed in Escherichia coli, purified to homogeneity and crystallized using the sitting-drop vapour-diffusion method. The NDK crystal diffracted to 2.2 Å resolution and belonged to the trigonal crystal system, with unit-cell parameters a = 114.2, c = 93.9 Å. Translation-function calculations yielded an unambiguous solution in the enantiomorphic space group P3221. (Source: Acta Crystallographi... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946510 Fri, 30 Oct 2009 00:00:00 +0100 2946510 http://www.medworm.com/index.php?rid=2946509&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fen5385 An atypical two-cysteine peroxidase, SAOUHSC_01822, from the virulent Staphylococcus aureus strain NCTC 8325 plays a major role in the reponse of the bacterium to oxidative stress. The protein was cloned, expressed, purified to homogeneity and crystallized. The protein was crystallized from 2 M ammonium sulfate, 0.1 M Na HEPES pH 7, 2%(v/v) PEG 400. A complete diffraction data set was collected to 2.3 Å resolution using a Rigaku MicroMax HF007 Cu Kα X-ray generator and a Rigaku R-AXIS IV++ detector. The crystals belonged to space group P21, with unit-cell parameters a = 43.50, b = 149.35, c = 73.73 Å, β = 104.4°, and contained four molecules in the asymmetric unit. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946509 Fri, 30 Oct 2009 00:00:00 +0100 2946509 http://www.medworm.com/index.php?rid=2946508&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fll5189 In this study, GmhA has been cloned, expressed, purified and crystallized. Synchrotron X-ray data were also collected to 1.9 Å resolution. The crystal belonged to the primitive orthorhombic space group P212121, with unit-cell parameters a = 61.3, b = 84.2, c = 142.3 Å. A full structural determination is under way in order to provide insights into the structure–function relationships of this protein. (Source: Acta Crystallographica Section F) Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946508 Fri, 30 Oct 2009 00:00:00 +0100 2946508 http://www.medworm.com/index.php?rid=2946507&cid=s_37344_60_f&fid=37344&url=http%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fgj5068 The bone morphogenetic protein (BMP) signalling pathway regulates diverse processes such as cell differentiation, anterior/posterior axis specification, cell growth and the formation of extra-embryonic tissues. The transcription factor Smad1 relays the BMP signal from the cytoplasm to the nucleus, where it binds short DNA-sequence motifs and regulates gene expression. However, how Smad1 selectively targets particular genomic regions is poorly understood. In order to understand the physical basis of the specific interaction of Smad1 with DNA and to contrast it with the highly homologous but functionally distinct Smad3 protein, the DNA-binding Mad-homology 1 (MH1) domain of Smad1 was cocrystallized with a 17-mer palindromic Smad-binding element (SBE). The extensive optimizations of the lengt... Acta Crystallographica Section F journals http://www.medworm.com/rss/comments.php?id=2946507 Fri, 30 Oct 2009 00:00:00 +0100 2946507