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At least 1,639 records · Page 91Linked to original sources
PubMed1999

Structural investigation of the negative-thermal-expansion material ZrW2O8.

High-resolution powder diffraction data have been recorded on cubic ZrW(2)O(8) [a = 9.18000 (3) Å at 2 K] at 260 temperatures from 2 to 520 K in 2 K steps. These data have confirmed that alpha-ZrW(2)O(8) has a negative coefficient of thermal expansion, alpha = -9.07 x 10(-6) K(-1) (2-350 K). A 'parametric' approach to Rietveld refinement is adopted and it is demonstrated that a full anisotropic refinement can be performed at each temperature, despite using a data collection time of only 5 min. Examination of the resulting structural parameters suggests that the origin of the contraction with increasing temperature can be traced straightforwardly to the rigid-body transverse librations of bridging O atoms. alpha-ZrW(2)O(8) undergoes a phase transition from P2(1)3 to Pa3; at 448 K that is associated with the onset of considerable oxygen mobility. The phase transition can be described in terms of a simple cubic three-dimensional Ising model. Unusual kinetics are associated with this phase transition. Hysteresis in the cell parameter through the phase transition is the opposite of that normally observed.

Journal Article↗
PubMed2000

Crystallization and preliminary X-ray analysis of high-alkaline pectate lyase.

Pel-15, a high-alkaline pectate lyase (pectate transeliminase; E.C. 4.2.2.2) from Bacillus sp. strain KSM-P15, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. Two different crystal forms were obtained and preliminary X-ray diffraction data were collected from each crystal form at 100 K. Both forms belong to the orthorhombic space group P2(1)2(1)2(1) and contain one molecule per asymmetric unit. The unit-cell parameters of form I are a = 43.2 (2), b = 60.2 (2), c = 82.2 (2) A and those of form II are a = 42.9 (1), b = 43.4 (1), c = 105.9 (3) A. Diffraction data to a resolution of 1.5 A were collected from form II crystals using a synchrotron-radiation source.

Bacillus↗
PubMed2001

Crystallization and preliminary X-ray analysis of (R)-specific enoyl-CoA hydratase from Aeromonas caviae involved in polyhydroxyalkanoate biosynthesis.

Dimeric (R)-specific enoyl-coenzyme A (CoA) hydratase from Aeromonas caviae catalyzes the hydration of trans-2-enoyl-CoAs with carbon lengths of 4-6 to yield their corresponding (R)-3-hydroxyacyl-CoAs and is essential for polyhydroxyalkanoate (PHA) biosynthesis. The enzyme has been crystallized by vapour diffusion against a reservoir solution containing 20% polyethylene glycol 4000, 5% 2-propanol and 20 mM HEPES pH 7.0 at 298 K. Crystals belong to the monoclinic space group C2, with unit-cell parameters a = 111.54 (3), b = 59.29 (1), c = 47.27 (4) A, beta = 113.04 (2) degrees and contain a dimeric molecule in the asymmetric unit. Flash-cooling of a crystal at 100 K alters its unit-cell parameters to a = 109.82 (7), b = 57.98 (6), c = 46.84 (2) A, beta = 112.71 (3) degrees. Native data to a resolution of 1.7 A have been collected with 94.5% completeness and an R(merge) of 4.0% under cryogenic (100 K) conditions using synchrotron radiation.

Aeromonas↗
PubMed2001

Preparation and crystallization of the stimulatory and inhibitory complexes of GTP cyclohydrolase I and its feedback regulatory protein GFRP.

Mammalian GTP cyclohydrolase I is a decameric enzyme in the first and rate-limiting step in the biosynthesis of tetrahydrobiopterin, which is an essential cofactor for enzymes producing neurotransmitters such as catecholamines and for nitric oxide synthases. The enzyme is dually regulated by its feedback regulatory protein GFRP in the presence of its stimulatory effector phenylalanine and its inhibitory effector biopterin. Here, both the stimulatory and inhibitory complexes of rat GTP cyclohydrolase I bound to GFRP were crystallized by vapour diffusion. Diffraction data sets at resolutions of 3.0 and 2.64 A were collected for the stimulatory and inhibitory complexes, respectively. Each complex consists of two GTPCHI pentamer rings and two GFRP pentamer rings, with pseudo-52 point-group symmetry.

Animals↗
PubMed2001

Crystallization and preliminary X-ray analysis of RecG, a replication-fork reversal helicase from Thermotoga maritima complexed with a three-way DNA junction.

The monomeric 3'-5' helicase RecG from the thermophilic bacterium Thermotoga maritima has been crystallized in complex with a three-way DNA junction, the preferred physiological substrate. The crystals were obtained by hanging-drop vapour diffusion. The crystals belong to space group C2, with unit-cell parameters a = 133.7, b = 144.6, c = 84.0 A, beta = 113.8 degrees. Native data to a resolution of 3.25 A were collected from crystals flash-cooled to 100 K.

Bacterial Proteins↗
PubMed2002

The three-dimensional structure of calcium-depleted human C-reactive protein from perfectly twinned crystals.

C-reactive protein is a member of the pentraxin family of oligomeric serum proteins which has been conserved through evolution, homologues having been found in every species in which they have been sought. Human C-reactive protein (hCRP) is the classical acute-phase reactant produced in large amounts in response to tissue damage and inflammation and is used almost universally as a clinical indicator of infection and inflammation. The role of hCRP in host defence and the calcium-dependent ligand-binding specificity of hCRP for phosphocholine moieties have long been recognized. In order to clarify the structural rearrangements associated with calcium binding, the reported affinity of calcium-depleted hCRP for polycations and other ligands, and the role of calcium in protection against denaturation and proteolysis, the structure of calcium-depleted hCRP has been determined by X-ray crystallography. Crystals of calcium-depleted hCRP are invariably twinned and those suitable for analysis are merohedral type II twins of point group 4 single crystals. The structure has been solved by molecular replacement using the calcium-bound hCRP structure [Shrive et al. (1996), Nature Struct. Biol. 3, 346-354]. It reveals two independent pentamers which form a face-to-face decamer across a dyad near-parallel to the twinning twofold axis. Cycles of intensity deconvolution, density modification (tenfold NCS) and model building, eventually including refinement, give a final R factor of 0.19 (R(free) = 0.20). Despite poor definition in some areas arising from the limited resolution of the data and from the twinning and disorder, the structure reveals the probable mode of twinning and the conformational changes, localized in one of the calcium-binding loops, which accompany calcium binding.

Binding Sites↗
PubMed2002

Purification, crystallization and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis, the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.

The vancomycin class of antibiotics is regarded as the last line of defence against Gram-positive bacteria. The compounds used clinically are very complex organic molecules and are made by fermentation. The biosynthesis of these is complex and fascinating. Its study holds out the prospect of utilizing genetic engineering of the enzymes in the pathway in order to produce novel vancomycin analogues. In part, this requires detailed structural insight into substrate specificity as well as the enzyme mechanism. The crystallization of one of the enzymes in the chloroeremomycin biosynthetic pathway (a member of the vancomycin family), dTDP-3-amino-4-keto 2,3,6-trideoxy-3-C-methyl-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis, is reported here. The protein is fourth in the pathway which makes a carbohydrate essential for the activity of chloroeremomycin. The crystals of EvaD diffract to 1.5 A and have unit-cell parameters a = 98.6, b = 72.0, c = 57.1 A with space group P2(1)2(1)2. Data to this resolution were collected at the European Synchrotron Radiation Facility.

Actinomycetales↗
PubMed2002

Crystallization and preliminary X-ray diffraction studies of the water-soluble state of the pore-forming toxin sticholysin II from the sea anemone Stichodactyla helianthus.

Sticholysin II (StnII) is a potent cytolytic protein produced by the sea anemone Stichodactyla helianthus. StnII belongs to the actinoporin family, a group of proteins which are characterized by their ability to spontaneously interact with biological membranes. The cytolytic character of these proteins is currently explained in terms of a molecular mechanism involving the formation of transmembrane pores. StnII has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality crystals have unit-cell parameters a = 32.30, b = 119.73, c = 43.42 A, beta = 90.04 degrees and belong to the monoclinic space group P2(1). Diffraction data to a resolution of 1.71 A were collected at synchrotron facilities.

Animals↗
PubMed2002

Crystallization and preliminary X-ray diffraction studies of the complete modular endolysin from Cp-1, a phage infecting Streptococcus pneumoniae.

Endolysin from the phage Cp-1 (Cpl-1) cleaves the glycosidic beta1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the pneumococcal cell wall. Cpl-1 has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality orthorhombic crystals of the native protein were obtained only after addition of the detergent n-decyl-beta-D-maltoside. Crystals belong to space group C222(1), with unit-cell parameters a = 77.949, b = 95.782, c = 129.282 A. Diffraction data to a resolution of 2.1 A were collected at a synchrotron facility.

Crystallization↗
PubMed2002

Cloning, purification and crystallization of full-length human annexin 2.

Annexin 2, a Ca(2+)/phospholipid-binding protein, is involved in many biological processes, including membrane aggregation and the modulation of fibrinolytic activity. Here, the expression and purification of recombinant full-length human annexin 2 is reported, as well as crystals obtained by sitting-drop and hanging-drop vapor diffusion at 277 K. A condition consisting of 18% PEG 8000, 0.1 M sodium cacodylate pH 6.5, 0.2 M calcium acetate yielded long needles that diffracted to 3.20 A. Another condition, consisting of 2.5 M NaCl, 0.1 M acetate pH 4.5, 0.2 M Li(2)SO(4), gave crystals with unit-cell parameters a = 48.36, b = 62.86, c = 119.11 A that diffracted to 1.52 A. Both crystals belong to the orthorhombic P2(1)2(1)2(1) space group. The high-resolution 1.52 A data set was collected at ALS beamline 5.0.2 and is 93.0% complete, with an R(sym) of 4.5%. The structure of full-length annexin 2 will provide insight into how its N-terminal domain contributes to its functional role in a variety of biological processes.

Annexin A2↗
PubMed2003

An unfolding/refolding step helps in the crystallization of a poorly soluble protein.

Proteins that are unstable or poorly soluble often elude crystallization. Here, a novel strategy is presented that leads to the crystallization of the isolated N-terminal propeptide of human procathepsin S, a proteinase belonging to the cathepsin L-like endopeptidases of the clan CA1 cysteine peptidases. Being very hydrophobic, the propeptide is extremely poorly soluble in aqueous solvents at neutral pH. Solubility is much better at acidic pH, but the native structure is destroyed under these conditions. A novel approach to the crystallization of this poorly soluble protein is presented in which it is first unfolded in an acidic buffer (pH 4.5) and then mixed with a nearly neutral crystallization buffer (pH 6.75) in which the native conformation should form spontaneously. Crystals were grown at a high concentration of MES (1.14 M) with 10% 2-propanol as precipitant. They belong to a tetragonal space group, with unit-cell parameters a = b = 151.1, c = 75.8 A. Diffraction data to a resolution of 3.5 A were obtained.

Cathepsins↗
PubMed2003

Crystallization and preliminary crystallographic studies on the extrinsic 23 kDa protein in the oxygen-evolving complex of photosystem II.

The extrinsic 23 kDa protein in the oxygen-evolving complex (OEC23 or PsbP) of photosystem II (PS II) helps to retain calcium and chloride ions, which are essential cofactors for the photosynthetic evolution of oxygen. OEC23 is found in the PS II complex from higher plants and green algae, but not in that from cyanobacteria or other ancestral photosynthetic organisms. In order to elucidate the three-dimensional structure and its molecular evolution, OEC23 was crystallized by the hanging-drop vapour-diffusion technique with PEG 4000 as a precipitant. Diffraction data to a resolution of 2.0 A were collected from a native crystal belonging to space group P2(1)2(1)2, with unit-cell parameters a = 91.36, b = 74.15, c = 52.16 A.

Crystallization↗
PubMed2003

Bacterial expression, purification and preliminary X-ray crystallographic characterization of the invertase inhibitor Nt-CIF from tobacco.

Acid invertases catalyzing the breakdown of sucrose are regulated at the post-translational level by extracellular inhibitory proteins of 16-20 kDa molecular weight in a pH-dependent manner. Little is known about the characteristics of the underlying protein-protein interaction. Here, the expression, purification, characterization, crystallization and initial X-ray analysis of a biologically active invertase inhibitor Nt-CIF from tobacco is reported. Four crystal forms covering a wide pH range have been obtained and data sets at resolutions higher than 2.5 A have been collected.

Cloning, Molecular↗
PubMed2004

Purification, partial characterization, crystallization and structural determination of AHP-LAAO, a novel L-amino-acid oxidase with cell apoptosis-inducing activity from Agkistrodon halys pallas venom.

A snake-venom protein named AHP-LAAO has been purified from Agkistrodon halys pallas venom using four-stage chromatography. AHP-LAAO is a novel member of the snake-venom L-amino-acid oxidase family. Its amino-acid sequence shows high homology to other members of this family. For L-leucine, the values of k(cat) and K(M) are 31.1 s(-1) and 0.25 mM, respectively. The molecular weight of AHP-LAAO is about 60.7 kDa as determined by MALDI-TOF mass spectrometry. AHP-LAAO can also induce apoptosis of cultured Hela cells. Two sets of diffraction data with similar resolution limits (about 2.5 A) were collected independently at MacCHESS (Cornell High Energy Synchrotron Source, USA) and IHEP (Institute of High Energy Physics, Beijing, China). The crystals belong to space group I2(1)3, with unit-cell parameter a = 169.31 A, corresponding to one molecule in the asymmetric unit and a volume-to-weight ratio of 3.33 A(3) Da(-1). The final structural model is similar to that of L-amino-acid oxidase from Calloselasma rhodostoma venom.

Amino Acid Oxidoreductases↗
PubMed2004

Purification, crystallization and preliminary X-ray analysis of uridine phosphorylase from Salmonella typhimurium.

The structural udp gene encoding uridine phosphorylase (UPh) was cloned from the Salmonella typhimurium chromosome and overexpressed in Escherichia coli cells. S. typhimurium UPh (StUPh) was purified to apparent homogeneity and crystallized. The primary structure of StUPh has high homology to the UPh from E. coli, but the enzymes differ substantially in substrate specificity and sensitivity to the polarity of the medium. Single crystals of StUPh were grown using hanging-drop vapor diffusion with PEG 8000 as the precipitant. X-ray diffraction data were collected to 2.9 A resolution. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group P6(1(5)), with unit-cell parameters a = 92.3, c = 267.5 A. The solvent content is 37.7% assuming the presence of one StUPh hexamer per asymmetric unit.

Cloning, Molecular↗
PubMed2004

Expression, purification and preliminary X-ray diffraction analysis of a ketoreductase from a type II polyketide synthase.

Polyketide metabolites produced by bacteria and other organisms include antibiotics, anticancer and antifungal compounds. In type II polyketide synthesis, three enzymes are sufficient to form a polyketide product of the requisite chain length, although the fidelity of the first cyclization is variable. Addition of ketoreductase (KR) to this system results in the formation of a product with correct cyclization and reduction. This paper reports the cloning of the Streptomyces coelicolor actIII ORF5 gene that codes for the ketoreductase. The 261-amino-acid protein has been overexpressed with a 20-residue His tag, purified by affinity chromatography and crystallized in space group P3(2)21, with unit-cell parameters a = b = 103.9, c = 123.1 angstroms. The crystals diffract to 2.5 angstroms resolution. A complete data set has been collected and structure solution and refinement is under way.

3-Oxoacyl-(Acyl-Carrier-Protein) Reductase↗
PubMed2004

Solution and structure of an alternating D,L-peptide.

The crystal structure of H-(L-Tyr-D-Tyr)(4)-L-Lys-OH has been determined to 1.3 A resolution. The D,L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) A. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel beta-helix. The structure has been solved by SIRAS using a crystal soaked in an iodide-containing solution for 1 min. The programs SHELXD and SHELXE were used to determine the iodide substructure and also the experimental electron-density map. Using the coordinates of known D,L-peptides deposited in the PDB, several attempts were made to solve the structure by molecular-replacement techniques. Although the backbone of the MR model selected shows great similarity and was used to trace the actual peptide structure in the map, it was not possible to obtain the correct solution before the experimental phases became available. The correct fragment orientations are easily determined, but the same does not apply to the translation search. Nevertheless, insights into fragment search and expansion were gained from the tests described in this paper. The correlation coefficient calculated with the resolution shell of data around 2.4 A, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments.

Crystallography, X-Ray↗
PubMed2006

Assessment of automatic ligand building in ARP/wARP.

The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.

Algorithms↗