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Improving diffraction by humidity control: a novel device compatible with X-ray beamlinesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dehydration of protein crystals is rarely used, despite being a post-crystallization method that is useful for the improvement of crystal diffraction properties, as it is difficult to reproduce and monitor. A novel device for hydration control of macromolecular crystals in a standard data-collection environment has been developed. The device delivers an air stream of precise relative humidity that can be used to alter the amount of water in macromolecular crystals. The device can be rapidly installed and is fully compatible with most standard synchrotron X-ray beamlines. Samples are mounted in cryoloops and the progress of...
Source: Acta Crystallographica Section D - November 18, 2009 Category: Biochemistry Authors: Sanchez-Weatherby, J.Bowler, M.W.Huet, J.Gobbo, A.Felisaz, F.Lavault, B.Moya, R.Kadlec, J.Ravelli, R.B.G.Cipriani, F. Tags: humidity-control device X-ray diffraction improvement crystallographic synchrotron instrumentation crystal dehydration research papers Source Type: journals

Notes of a protein crystallographer: the molecular structure of evolutionary theoryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Some of the current trends in the structure of evolutionary biology are reviewed using as a framework the book of the same title by S. J. Gould (1941–2002). The revised concepts and interpretations of the structure–function relationship in evolutionary biology are discussed in relation to the past achievements and future developments in structural biology. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Abad-Zapatero, C. Tags: Evolutionary theory evolution of protein structure evolution of molecular structure adaptationism evolutionary constraints essays Source Type: journals

A case of structure determination using pseudosymmetryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson ...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Radaev, S.Agniswamy, J.Sun, P.D. Tags: pseudosymmetry structure determination cysteine proteases Mac-1 short communications Source Type: journals

Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without divalent cations were solved at 2.17 and 2.00 Å resolution, respectively. HindIII forms a dimer. The structures showed that HindIII belongs to the EcoRI-like (α-class) subfamily of type II restriction endonucleases. The cognate DNA-complex structures revealed the specific DNA-recognition mechanism of HindIII by which it recognizes the palindromic sequence A/AGCTT. In the Mg2+ ion-soaked structure the DNA was cleaved and two ions were bound at each active site, corresponding to the two-metal-ion mechanism. (Source: Acta Crysta...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Watanabe, N.Takasaki, Y.Sato, C.Ando, S.Tanaka, I. Tags: restriction endonucleases DNA complex vaporizing-iodine labelling method research papers Source Type: journals

Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp. C-1: towards understanding the mechanism of the closure of the interdomain cleftEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
NAD+-dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD+ to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95 Å resolution, respectively. MorFDH is similar to the previously studied FDH from the bacterium Pseudomonas sp. 101 in overall structure, cofactor-binding mode and active-site architecture, but differs in that the eight-residue-longer C-terminal fragment is visible in the electron-density maps of MorFDH. MorFDH also differs in the org...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Shabalin, I.G.Filippova, E.V.Polyakov, K.M.Sadykhov, E.G.Safonova, T.N.Tikhonova, T.V.Tishkov, V.I.Popov, V.O. Tags: NAD -dependent formate dehydrogenases protein conformation interdomain cleft dimer interface apo and holo forms research papers Source Type: journals

The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site grooveEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Glycoside hydrolase family 13 (GH-13) mainly contains starch-degrading or starch-modifying enzymes. Sucrose hydrolases utilize sucrose instead of amylose as the primary glucosyl donor. Here, the catalytic properties and X-ray structure of sucrose hydrolase from Xanthomonas campestris pv. campestris are reported. Sucrose hydrolysis catalyzed by the enzyme follows Michaelis–Menten kinetics, with a Km of 60.7 mM and a kcat of 21.7 s−1. The structure of the enzyme was solved at a resolution of 1.9 Å in the resting state with an empty active site. This represents the first apo structure from subfamily 4 of GH-13. Com...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Champion, E.Remaud-Simeon, M.Skov, L.K.Kastrup, J.S.Gajhede, M.Mirza, O. Tags: glycoside hydrolase family 13 sucrose hydrolysis active-site conformation reaction mechanism research papers Source Type: journals

Structure of the Taz2 domain of p300: insights into ligand bindingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CBP and its paralog p300 are histone acetyl transferases that regulate gene expression by interacting with multiple transcription factors via specialized domains. The structure of a segment of human p300 protein (residues 1723–1836) corresponding to the extended zinc-binding Taz2 domain has been investigated. The crystal structure was solved by the SAD approach utilizing the anomalous diffraction signal of the bound Zn ions. The structure comprises an atypical helical bundle stabilized by three Zn ions and closely resembles the solution structures determined previously for shorter peptides. Residues 1813–1834 from t...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Miller, M.Dauter, Z.Cherry, S.Tropea, J.E.Wlodawer, A. Tags: zinc-finger proteins anomalous diffraction protein recognition transcription regulation research papers Source Type: journals

Structure of the X (ADRP) domain of nsp3 from feline coronavirusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2 Å resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9 Å resolution. The structure of the FCoV X domain had the expected ...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Wojdyla, J.A.Manolaridis, I.Snijder, E.J.Gorbalenya, A.E.Coutard, B.Piotrowski, Y.Hilgenfeld, R.Tucker, P.A. Tags: feline coronavirus X domains ADRP domains nonstructural protein 3 research papers Source Type: journals

On the use of logarithmic scales for analysis of diffraction dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Predictions of the possible model parameterization and of the values of model characteristics such as R factors are important for macromolecular refinement and validation protocols. One of the key parameters defining these and other values is the resolution of the experimentally measured diffraction data. The higher the resolution, the larger the number of diffraction data Nref, the larger its ratio to the number Nat of non-H atoms, the more parameters per atom can be used for modelling and the more precise and detailed a model can be obtained. The ratio Nref/Nat was calculated for models deposited in the Protein Data Ban...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Urzhumtsev, A.Afonine, P.V.Adams, P.D. Tags: resolution logarithmic scale R factor data-to-parameter ratio research papers Source Type: journals

A systematic study of 50S ribosomal subunit purification enabling robust crystallizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A systematic analysis was undertaken to seek correlations between the integrity, purity and activity of 50S ribosomal subunit preparations from Deinococcus radiodurans and their ability to crystallize. Conditions of fermentation, purification and crystallization were varied in a search for crystals that could reliably supply an industrial X-ray crystallography program for the structure-based design of ribosomal antibiotics. A robust protocol was obtained to routinely obtain crystals that gave diffraction patterns extending to 2.9 Å resolution and that were large enough to yield a complete data set from a single crystal....
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: McLellan, T.J.Marr, E.S.Wondrack, L.M.Subashi, T.A.Aeed, P.A.Han, S.Xu, Z.Wang, I.-K.Maguire, B.A. Tags: ribosome 50S subunit crystallization purification mass spectrometry Deinococcus radiodurans research papers Source Type: journals

Structure of laminin-binding adhesin (Lmb) from Streptococcus agalactiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Adhesion/invasion of pathogenic bacteria is a critical step in infection and is mediated by surface-exposed proteins termed adhesins. The crystal structure of recombinant Lmb, a laminin-binding adhesin from Streptococcus agalactiae, has been determined at 2.5 Å resolution. Based on sequence and structural homology, Lmb was placed into the cluster 9 family of the ABC (ATP-binding cassette) transport system. The structural organization of Lmb closely resembles that of ABC-type solute-binding proteins (SBPs), in which two structurally related globular domains interact with each other to form a metal-binding cavity at the...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Ragunathan, P.Spellerberg, B.Ponnuraj, K. Tags: adhesins metal transporters surface proteins laminin binding ATP-binding cassette solute-binding proteins research papers Source Type: journals

Structure of Helicobacter pyloril-asparaginase at 1.4 Å resolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacterial l-asparaginases have been used in the treatment of childhood acute lymphoblastic leukaemia for over 30 years. Their therapeutic effect is based on their ability to catalyze the conversion of l-asparagine, an essential amino acid in certain tumours, to l-aspartic acid and ammonia. Two l-asparaginases, one from Escherichia coli and the other from Erwinia chrysanthemi, have been widely employed in clinical practice as anti-leukaemia drugs. However, l-asparaginases are also able to cause severe side effects owing to their intrinsic glutaminase activity. Helicobacter pylori l-asparaginase (HpA) has been reported to ...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Dhavala, P.Papageorgiou, A.C. Tags: l-asparaginases active site leukaemia treatment therapeutic enzymes research papers Source Type: journals

The effect of a proline residue on the rate of growth and the space group of α-spectrin SH3-domain crystalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
α-Spectrin SH3-domain (Spc-SH3) crystallization is characterized by very fast growth of the crystals in the presence of ammonium sulfate as a precipitant agent. The origin of this behaviour can be attributed to the presence of a proline residue that participates in a crystal contact mimicking the binding of proline-rich sequences to SH3 domains. This residue, Pro20, is located in the RT loop and is the main contact in one of the interfaces present in the orthorhombic Spc-SH3 crystal structures. In order to understand the molecular interactions that are responsible for the very fast crystal growth of the wild-type (WT) Spc...
Source: Acta Crystallographica Section D - November 17, 2009 Category: Biochemistry Authors: Cámara-Artigas, A.Andújar-Sánchez, M.Ortiz-Salmerón, E.Cuadri, C.Casares, S. Tags: SH3 domains nucleation crystallization mechanism research papers Source Type: journals

The effect of protein–precipitant interfaces and applied shear on the nucleation and growth of lysozyme crystalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper is concerned with the effect of protein–precipitant interfaces and externally applied shear on the nucleation and growth kinetics of hen egg-white lysozyme crystals. The early stages of microbatch crystallization of lysozyme were explored using both optical and confocal fluorescence microscopy imaging. Initially, an antisolvent (precipitant) was added to a protein drop and the optical development of the protein–precipitant interface was followed with time. In the presence of the water-soluble polymer poly(ethylene glycol) (PEG) a sharp interface was observed to form immediately within the drop, giving an ini...
Source: Acta Crystallographica Section D - October 23, 2009 Category: Biochemistry Authors: Reis, N.M.Chirgadze, D.Y.Blundell, T.L.Mackley, M.R. Tags: lysozyme crystallization nucleation growth shear interfaces instabilities concentration gradients research papers Source Type: journals

Dwelling in the dark: procedures for the crystallography of phytochromes and other photochromic proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Crystallization of phytochromes and other photochromic proteins is hampered by the conformational changes that they undergo on exposure to light. As a canonical phytochrome, cyanobacterial Cph1 switches between two stable states upon absorption of red/far-red light. Consequently, it is mandatory to work in darkness from protein purification to crystal cryoprotection in order to ensure complete occupancy of one state or the other. With the simple and inexpensive methods that have been developed, phytochromes and other photochromic molecules can effectively be handled and crystallized, as has been demonstrated by the solutio...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Mailliet, J.Psakis, G.Schroeder, C.Kaltofen, S.Dürrwang, U.Hughes, J.Essen, L.-O. Tags: phytochromes photochromic proteins crystallization short communications Source Type: journals

A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall kcat. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbation...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Lyubimov, A.Y.Chen, L.Sampson, N.S.Vrielink, A. Tags: GMC oxidoreductases site-directed mutagenesis hydrophobic tunnel flavoproteins research papers Source Type: journals

Structure of the human filamin A actin-binding domainEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Filamin A (FLNa) is a large dimeric protein that binds to actin filaments via its actin-binding domain (ABD). The crystal structure of this domain was solved at 3.2 Å resolution. The domain adopts a closed conformation typical of other ABDs, but also forms a dimer both in crystallization conditions and in solution. The structure shows the localization of the residues mutated in patients with periventricular nodular heterotopia or otopalatodigital syndrome. Structural analysis predicts that mutations in both types of disorder may affect actin binding. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Ruskamo, S.Ylänne, J. Tags: filamin actin-binding protein calponin-homology domain patient mutations research papers Source Type: journals

Direct-method SAD phasing of proteins enhanced by the use of intrinsic bimodal phase distributions in the subsequent phase-improvement processEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A modified SAD (single-wavelength anomalous diffraction) phasing algorithm has been introduced in the latest version of the program OASIS. In addition to direct-method phases and figures of merit, Hendrickson–Lattman coefficients that correspond to the original unresolved bimodal phase distributions are also output and used in subsequent phase-improvement procedures in combination with the improved phases. This provides the possibility of rebreaking the SAD phase ambiguity using the ever-improving phases resulting from the phase-improvement process. Tests using experimental SAD data from six known proteins showed that i...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Wu, L.-J.Zhang, T.Gu, Y.-X.Zheng, C.-D.Fan, H.-F. Tags: OASIS SAD phasing proteins research papers Source Type: journals

Structure of the major carrot allergen Dau c 1Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dau c 1 is a major allergen of carrot (Daucus carota) which displays IgE cross-reactivity with the homologous major birch-pollen allergen Bet v 1. The crystal structure of Dau c 1 has been determined to a resolution of 2.7 Å, revealing tight dimers. The structure of Dau c 1 is similar to those of the major allergens from celery, Api g 1, and birch pollen, Bet v 1. Electron density has been observed in the hydrophobic cavity of each monomer and has been modelled with polyethylene glycol oligomers of varying length. Comparison of the surface topology and physicochemical properties of Dau c 1 an...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Marković-Housley, Z.Basle, A.Padavattan, S.Maderegger, B.Schirmer, T.Hoffmann-Sommergruber, K. Tags: major carrot allergen Dau c 1 cross-reactivity immunotherapy research papers Source Type: journals

Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lignin biodegradation, a key step in carbon recycling in land ecosystems, is carried out by white-rot fungi through an H2O2-dependent process defined as enzymatic combustion. Pleurotus eryngii is a selective lignin-degrading fungus that produces H2O2 during redox cycling of p-anisylic compounds involving the secreted flavoenzyme aryl-alcohol oxidase (AAO). Here, the 2.4 Å resolution X-ray crystal structure of this oxidoreductase, which catalyzes dehydrogenation reactions on various primary polyunsaturated alcohols, yielding the corresponding aldehydes, is reported. The AAO crystal structure was solved by single-wavelen...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Fernández, I.S.Ruíz-Dueñas, F.J.Santillana, E.Ferreira, P.Martínez, M.J.Martínez, Á.T.Romero, A. Tags: aryl-alcohol oxidases GMC oxidoreductase family Pleurotus eryngii research papers Source Type: journals

Structure of cyclophilin from Leishmania donovani bound to cyclosporin at 2.6 Å resolution: correlation between structure and thermodynamic dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Drug development against Leishmania donovani, the pathogen that causes visceral leishmaniasis in humans, is currently an active area of research given the widespread prevalence of the disease and the emergence of resistant strains. The immunosuppressive drug cyclosporin is known to have antiparasitic activity against a variety of pathogens. The receptor for cyclosporin is the protein cyclophilin, which is a ubiquitous peptidylprolyl isomerase. The crystal structure of cyclophilin from L. donovani complexed with cyclosporin has been solved at 2.6 Å resolution. The thermodynamic parameters of the interaction have been de...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Venugopal, V.Datta, A.K.Bhattacharyya, D.Dasgupta, D.Banerjee, R. Tags: cyclophilin cyclosporin Leishmania donovani research papers Source Type: journals

The structure of Mg-ATPase nucleotide-binding domain at 1.6 Å resolution reveals a unique ATP-binding motifEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The structure of the nucleotide-binding domain of the Mg-ATPase MgtA from Escherichia coli has been solved and refined to 1.6 Å resolution. The structure is made up of a six-stranded β-sheet and a bundle of three α-helices, with the nucleotide-binding site sandwiched in between. The MgtA nucleotide-binding domain is shorter and more compact compared with that of the related Ca-ATPase and lacks one of the β-strands at the edge of the β-sheet. The ATP-binding pocket is surrounded by three sequence and structural motifs known from other P-type ATPases and a fourth unique motif that is found only in Mg-ATPases. This mot...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Håkansson, K.O. Tags: P-type ATPases ATP binding MgtA MgtB membrane proteins research papers Source Type: journals

Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoproteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion co...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Lee, J.E.Fusco, M.L.Abelson, D.M.Hessell, A.J.Burton, D.R.Saphire, E.O. Tags: glycoproteins structure determination difficult structures antibody complexes viral proteins human proteins tactics to improve diffraction techniques for phase determination deglycosylation model building research papers Source Type: journals

Protein flexibility: coordinate uncertainties and interpretation of structural differencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between ...
Source: Acta Crystallographica Section D - October 21, 2009 Category: Biochemistry Authors: Rashin, A.A.Rashin, A.H.L.Jernigan, R.L. Tags: bioinformatics computation validation molecular machines rigid parts research papers Source Type: journals

Overproduction, purification and structure determination of human dual-specificity phosphatase 14Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dual-specificity phosphatases (DUSPs) are enzymes that participate in the regulation of biological processes such as cell growth, differentiation, transcription and metabolism. A number of DUSPs are able to dephosphorylate phosphorylated serine, threonine and tyrosine residues on mitogen-activated protein kinases (MAPKs) and thus are also classified as MAPK phosphatases (MKPs). As an increasing number of DUSPs are being identified and characterized, there is a growing need to understand their biological activities at the molecular level. There is also significant interest in identifying DUSPs that could be potential target...
Source: Acta Crystallographica Section D - September 16, 2009 Category: Biochemistry Authors: Lountos, G.T.Tropea, J.E.Cherry, S.Waugh, D.S. Tags: dual-specificity phosphatases MAPK phosphatases DUSP14 MKP6 research papers Source Type: journals

A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Ana...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Breustedt, D.A.Chatwell, L.Skerra, A. Tags: apolipoprotein D β -barrel 1,4-butanediol induced fit tear lipocalin von Ebner's gland protein research papers Source Type: journals

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a new algorithm for the automatic modelling of discrete heterogeneity is presented. At high resolution, the authors' single multi-conformer model, with correlated structural features to represent heterogeneity, shows improved agreement with the diffraction data compared with a single-conformer model. The model appears to be representative of the set of structures present in the crystal. In contrast, below 2 Å resolution representing ambiguous electron density by correlated multi-conformers in a single model does not yield better agreement with the experimental data. Consistent with previous studies, this ...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: van den Bedem, H.Dhanik, A.Latombe, J.-C.Deacon, A.M. Tags: heterogeneity modeling multi-conformers research papers Source Type: journals

Structure of d-alanine-d-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme–ligand interactionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
d-Alanine-d-alanine ligase (Ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. The enzyme catalyzes the condensation of two d-Ala molecules using ATP to produce d-Ala-d-Ala, which is the terminal peptide of a peptidoglycan monomer. The structures of five forms of the enzyme from Thermus thermophilus HB8 (TtDdl) were determined: unliganded TtDdl (2.3 Å resolution), TtDdl–adenylyl imidodiphosphate (2.6 Å), TtDdl–ADP (2.2 Å), TtDdl–ADP–d-Ala (1.9 Å) and TtDdl–ATP–d-Ala-d-Ala (2.3 Å). The central domain rotates as a rigid body towards the acti...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Kitamura, Y.Ebihara, A.Agari, Y.Shinkai, A.Hirotsu, K.Kuramitsu, S. Tags: d-alanine-d-alanine ligase Thermus thermophilus HB8 catalytic mechanism conformational change research papers Source Type: journals

On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determinationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A combination of molecular replacement and single-wavelength anomalous diffraction phasing has been incorporated into the automated structure-determination platform Auto-Rickshaw. The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building. The improvement over the standard SAD or MR approaches is illustrated by ten test cases taken from the JCSG diffraction data-set database. Poor MR or SAD phases with phase errors larger than 70° can be improved using the described procedure and a large fraction of the model can be determined in a pu...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Panjikar, S.Parthasarathy, V.Lamzin, V.S.Weiss, M.S.Tucker, P.A. Tags: automated structure determination molecular replacement single-wavelength anomalous diffraction research papers Source Type: journals

Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The stru...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Morgunova, E.Gray, F.C.MacNeill, S.A.Ladenstein, R. Tags: PCNA – DNA interactions sliding clamps halophilic environment research papers Source Type: journals

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses simple and fast quantum-chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow the attainment of a number of diverse goals including geometry optimization and generation of restraints. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Moriarty, N.W.Grosse-Kunstleve, R.W.Adams, P.D. Tags: ligands coordinates restraints Python object-oriented programming research papers Source Type: journals

Effects of impurities on membrane-protein crystallization in different systemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
When starting a protein-crystallization project, scientists are faced with several unknowns. Amongst them are these questions: (i) is the purity of the starting material sufficient? and (ii) which type of crystallization experiment is the most promising to conduct? The difficulty in purifying active membrane-protein samples for crystallization trials and the high costs associated with producing such samples require an extremely pragmatic approach. Additionally, practical guidelines are needed to increase the efficiency of membrane-protein crystallization. In order to address these conundrums, the effects of commonly encoun...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Kors, C.A.Wallace, E.Davies, D.R.Li, L.Laible, P.D.Nollert, P. Tags: membrane proteins impurities crystallization research papers Source Type: journals

A multivariate likelihood SIRAS function for phasing and model refinementEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A likelihood function based on the multivariate probability distribution of all observed structure-factor amplitudes from a single isomorphous replacement with anomalous scattering experiment has been derived and implemented for use in substructure refinement and phasing as well as macromolecular model refinement. Efficient calculation of a multidimensional integration required for function evaluation has been achieved by approximations based on the function's properties. The use of the function in both phasing and protein model building with iterative refinement was essential for successful automated model building in the...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Skubák, P.Murshudov, G.Pannu, N.S. Tags: multivariate normal probability distribution single isomorphous replacement with anomalous scattering experimental phasing direct incorporation of prior phase information research papers Source Type: journals

A neutron crystallographic analysis of T6 porcine insulin at 2.1 Å resolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Neutron diffraction data for T6 porcine insulin were collected to 2.1 Å resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structure was refined to a residual of 0.179. The hydrogen-bonding network of the central core of the hexamer was observed and the charge balance between positively charged Zn ions and their surrounding structure was interpreted by considering the protonation and/or deprotonation states and interactions of HisB10, water and GluB13. The observed double conformation of GluB13 was essen...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Iwai, W.Yamada, T.Kurihara, K.Ohnishi, Y.Kobayashi, Y.Tanaka, I.Takahashi, H.Kuroki, R.Tamada, T.Niimura, N. Tags: T6 insulin neutron crystallography protonation charge balance H/D exchange hydrogen bonds research papers Source Type: journals

End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, high-resolution structures of all-α proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N–N, N–C, C–C, N–MID and C–MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal intera...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Ghosh, T.S.Chaitanya, S.K.Sankararamakrishnan, R. Tags: helix-packing interactions – helix interfaces residue surface areas side-chain lengths interhelical hydrophobic contacts interhelical distances research papers Source Type: journals

Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Tbd_0210 gene of the chemolithotrophic bacterium Thiobacillus denitrificans is annotated to encode a 60.5 kDa bifunctional enzyme with ATP sulfurylase and APS kinase activity. This putative bifunctional enzyme was cloned, expressed and structurally characterized. The 2.95 Å resolution X-ray crystal structure reported here revealed a hexameric assembly with D3 symmetry. Each subunit contains a large N-terminal sulfurylase-like domain and a C-terminal APS kinase domain reminiscent of the two-domain fungal ATP sulfurylases of Penicillium chrysogenum and Saccharomyces cerevisiae, which also exhibit a hexameric assembl...
Source: Acta Crystallographica Section D - September 15, 2009 Category: Biochemistry Authors: Gay, S.C.Segel, I.H.Fisher, A.J. Tags: APS kinases adenylylsulfate kinases ATP sulfurylases sulfate metabolism nucleotide kinase Thiobacillus denitrificans research papers Source Type: journals

ACORN2: new developments of the ACORN conceptEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The density-modification procedures incorporated in ACORN, available in the CCP4 package, have proved to be very successful in solving and refining high-resolution crystal structures from very poor starting sets. These can be calculated from a correctly positioned initial fragment containing between 1 and 8% of the scattering power of the total structure. Improvements of ACORN, reported here and incorporated in the program ACORN2, have lowered the size of the fragment required and examples are given of structures solved with only 0.25% of the scattering power in the fragment, which may be a single atom. Applications of ACO...
Source: Acta Crystallographica Section D - August 14, 2009 Category: Biochemistry Authors: Dodson, E.J.Woolfson, M.M. Tags: ACORN2 density modification phase refinement protein structure solution research papers Source Type: journals

Protein Crystallography – A Concise Guide. By Eaton E. Lattman and Patrick J. Loll. Baltimore, Maryland, USA: John Hopkins University Press, 2008. Pp. 136. Price (hardback) US$ 70. ISBN 9780801888069.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Scheidig A.J. Tags: book review book reviews Source Type: journals

On the packing structure of collagen: response to Okuyama et al.'s comment on Microfibrillar structure of type I collagen in situEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A response is published to the comment by Okuyama et al. [(2009) Acta Cryst. D65, 1007–1008] on Microfibrillar structure of type I collagen in situ. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Orgel, J.P.R.O. Tags: letters to the editor type I collagen Source Type: journals

Comment on Microfibrillar structure of type I collagen in situ by Orgel et al. (2006), Proc. Natl Acad. Sci. USA, 103, 9001–9005Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A comment is published on the article Microfibrillar structure of type I collagen in situ by Orgel et al. [(2006), Proc. Natl Acad. Sci. USA, 103, 9001–9005]. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Okuyama, K.Bächinger, H.P.Mizuno, K.Boudko, S.Engel, J.Berisio, R.Vitagliano, L. Tags: letters to the editor type I collagen Source Type: journals

To scavenge or not to scavenge: that is the questionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Analysis of a series of diffraction data sets measured from four native as well as four nicotinic acid-soaked crystals of trypsin at 100 K shows a high variability in radiation-sensitivity among individual crystals for both nicotinic acid-soaked and native crystals. The level of radiation-sensitivity and the extent of its variability is statistically indistinguishable between the two conditions. This suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation. This is in contrast to previous results [Kauffmann et...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Nowak, E.Brzuszkiewicz, A.Dauter, M.Dauter, Z.Rosenbaum, G. Tags: protein crystallography radiation damage scavengers nicotinic acid short communications Source Type: journals

Automatic implementation of precise grid screens: the four-corners methodEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Crystallization trials can be designed as a systematic gradient of the concentration of key reagents and/or pH centered on the original conditions. While the concept of the grid screen is simple, its implementation is tedious and difficult by hand. A procedure has been developed for preparing crystallization grid screens that is both efficient and achieves high accuracy because it relies on a limited number of solutions that are carefully prepared by hand. The `four-corners' approach to designing grid screens uses the minimum and maximum concentrations of the components being varied in the grid screen as the sole stock sol...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Hennessy, D.N.Narayanan, B.Rosenberg, J.M. Tags: crystallization grid screens pH robotics short communications Source Type: journals

Structure and epimerase activity of anthocyanidin reductase from Vitis viniferaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Together with leucoanthocyanidin reductase, anthocyanidin reductase (ANR) is one of the two enzymes of the flavonoid-biosynthesis pathway that produces the flavan-3-ol monomers required for the formation of proanthocyanidins or condensed tannins. It has been shown to catalyse the double reduction of anthocyanidins to form 2R,3R-flavan-3-ols, which can be further transformed to the 2S,3R isomers by non-enzymatic epimerization. ANR from grape (Vitis vinifera) was expressed in Escherichia coli and purified. Unexpectedly, RP-HPLC, LC-MS and NMR experiments clearly established that the enzyme produces a 50:50 mixture of 2,3-cis...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Gargouri, M.Manigand, C.Maugé, C.Granier, T.Langlois d'Estaintot, B.Cala, O.Pianet, I.Bathany, K.Chaudière, J.Gallois, B. Tags: flavonoid biosynthesis flavan-3-ols short-chain dehydrogenase reductases anthocyanidin reductases Vitis vinifera research papers Source Type: journals

Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1CEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lattice-translocation or crystal order–disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Tsai, Y.Sawaya, M.R.Yeates, T.O. Tags: translocation disorders hexamer carboxysome shell symmetry enhancement – modulated structures research papers Source Type: journals

Structure of the single-stranded DNA-binding protein from Streptomyces coelicolorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The crystal structure of the single-stranded DNA-binding protein (SSB) from Streptomyces coelicolor, a filamentous soil bacterium with a complex life cycle and a linear chromosome, has been solved and refined at 2.1 Å resolution. The three-dimensional structure shows a common conserved central OB-fold that is found in all structurally determined SSB proteins. However, it shows variations in quaternary structure that have previously only been found in mycobacterial SSBs. The strand involved in the clamp mechanism characteristic of this type of quaternary structure leads to higher stability of the homotetramer. To the bes...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Štefanić, Z.Vujaklija, D.Luić, M. Tags: single-stranded DNA-binding proteins SSBs Streptomyces coelicolor OB-fold research papers Source Type: journals

Application of general formulas for the correction of a lattice-translocation defect in crystals of a lentiviral integrase in complex with LEDGFEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this report, LTD theory is extended and a new general method for determining defect fractions is developed based on the heights of the non-origin peaks observed in native Patterson maps. The application of this method to crystals of lentiviral integrase in complex with its cofactor, where the observed translocation vector does not equal a small integral fraction of a unit-cell edge, is reported and its general application to all classic LTD cases is predicted. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Hare, S.Cherepanov, P.Wang, J. Tags: lattice-translocation defects lentiviral integrase research papers Source Type: journals

Polarizable atomic multipole X-ray refinement: application to peptide crystalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magn...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Schnieders, M.J.Fenn, T.D.Pande, V.S.Brunger, A.T. Tags: scattering factors aspherical anisotropic force fields multipole polarization AMOEBA bond density direct summation FFT SGFFT Ewald PME research papers Source Type: journals

Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
2,3-Diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1P enolase), a RuBisCO-like protein (RLP), catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate. The crystal structure of the apo decarbamylated form (E form) of Bacillus subtilis DK-MTP-1P enolase (Bs-DK-MTP-1P enolase) has been determined at 2.3 Å resolution. The overall structure of the E form of Bs-DK-MTP-1P enolase highly resembles that of Geobacillus kaustophilus DK-MTP-1P enolase (Gk-DK-MTP-1P enolase), with the exception of a few insertions or deletions and of a few residues at the active site. In the E form of Bs-DK-MTP-1P enolase, Lys1...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Tamura, H.Saito, Y.Ashida, H.Kai, Y.Inoue, T.Yokota, A.Matsumura, H. Tags: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase RuBisCO-like proteins research papers Source Type: journals

Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Thioredoxins (Trxs) are protein disulfide reductases that regulate the intracellular redox environment and are important for seed germination in plants. Trxs are in turn regulated by NADPH-dependent thioredoxin reductases (NTRs), which provide reducing equivalents to Trx using NADPH to recycle Trxs to the active form. Here, the first crystal structure of a cereal NTR, HvNTR2 from Hordeum vulgare (barley), is presented, which is also the first structure of a monocot plant NTR. The structure was determined at 2.6 Å resolution and refined to an Rcryst of 19.0% and an Rfree of 23.8%. The dimeric protein is structurally sim...
Source: Acta Crystallographica Section D - August 13, 2009 Category: Biochemistry Authors: Kirkensgaard, K.G.Hägglund, P.Finnie, C.Svensson, B.Henriksen, A. Tags: NADPH-dependent thioredoxin reductases disulfide oxidoreductases barley germination seed development redox regulation research papers Source Type: journals

A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 Å resolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 Å resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7 Å resolution. The protonation and deprotonation states of all of the charged amino-a...
Source: Acta Crystallographica Section D - August 6, 2009 Category: Biochemistry Authors: Yagi, D.Yamada, T.Kurihara, K.Ohnishi, Y.Yamashita, M.Tamada, T.Tanaka, I.Kuroki, R.Niimura, N. Tags: ribonuclease A neutron diffraction enzymatic mechanism protonation state hydrogen-bonding network research papers Source Type: journals