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Matthews Coefficient (Matthew + coefficient)
Terms modified by Matthews Coefficient Selected AbstractsOn the use of logarithmic scales for analysis of diffraction dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Alexandre Urzhumtsev Predictions of the possible model parameterization and of the values of model characteristics such as R factors are important for macromolecular refinement and validation protocols. One of the key parameters defining these and other values is the resolution of the experimentally measured diffraction data. The higher the resolution, the larger the number of diffraction data Nref, the larger its ratio to the number Nat of non-H atoms, the more parameters per atom can be used for modelling and the more precise and detailed a model can be obtained. The ratio Nref/Nat was calculated for models deposited in the Protein Data Bank as a function of the resolution at which the structures were reported. The most frequent values for this distribution depend essentially linearly on resolution when the latter is expressed on a uniform logarithmic scale. This defines simple analytic formulae for the typical Matthews coefficient and for the typically allowed number of parameters per atom for crystals diffracting to a given resolution. This simple dependence makes it possible in many cases to estimate the expected resolution of the experimental data for a crystal with a given Matthews coefficient. When expressed using the same logarithmic scale, the most frequent values for R and Rfree factors and for their difference are also essentially linear across a large resolution range. The minimal R -factor values are practically constant at resolutions better than 3,Å, below which they begin to grow sharply. This simple dependence on the resolution allows the prediction of expected R -factor values for unknown structures and may be used to guide model refinement and validation. [source] Crystallization and preliminary X-ray crystallographic analysis of a non-specific lipid-transfer protein with antipathogenic activity from Phaseolus mungoACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Shao-Yun Wang A 9,kDa non-specific lipid-transfer protein (nsLTP) from mung bean (Phaseolus mungo) seeds, displaying antifungal activity, antibacterial activity and lipid-transfer activity, was crystallized at 297,K using ammonium sulfate as a precipitant by means of the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to a resolution of 2.4,Å. The crystals are rhombohedral, belonging to space group P212121, with unit-cell parameters a = 38.671, b = 51.785, c = 55.925,Å. Assuming the presence of one molecule in the crystallographic asymmetric unit results in a Matthews coefficient (VM) of approximately 3.0,Å3,Da,1, corresponding to a solvent content of about 58%. [source] Cloning, expression, purification and crystallization of a transcriptional regulatory protein (Rv3291c) from Mycobacterium tuberculosis H37RvACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Tripti Shrivastava Rv3291c, the translational product of the Mycobacterium tuberculosisRv3291c gene, is an 18,kDa protein. It is a putative transcriptional regulatory protein belonging to the leucine-responsive regulatory protein/asparagine synthase C (Lrp/AsnC) family, which are proteins that have been identified in archaea and bacteria. Rv3291c probably plays a significant role during the persistent/latent phase of M. tuberculosis, as supported by its up-regulation several-fold during this stage. Orthorhombic crystals of recombinant Rv3291c have been grown from trisodium citrate dihydrate-buffered solutions containing monoammonium dihydrogen phosphate. Diffraction data extending to 2.7,Å have been collected from a single crystal with unit-cell parameters a = 99.6, b = 100.7, c = 100.6,Å. Assuming an octamer in the asymmetric unit results in a Matthews coefficient (VM) of 1.75,Å3,Da,1, corresponding to a solvent content of about 30%. [source] Purification, crystallization and preliminary X-ray crystallographic analysis of a cysteine-rich secretory protein (CRISP) from Naja atra venomACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Yu-Ling Wang Cysteine-rich secretory proteins (CRISPs) play an important role in the innate immune system and are transcriptionally regulated by androgens in several tissues. The proteins are mostly found in the epididymis and granules of mammals, whilst a number of snake venoms also contain CRISP-family proteins. The natrin protein from the venom of Naja atra (Taiwan cobra), which belongs to a family of CRISPs and has a cysteine-rich C-terminal amino-acid sequence, has been purified using a three-stage chromatography procedure and crystals suitable for X-ray analysis have been obtained using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.58,Å resolution using synchrotron radiation; the crystals belong to space group C2221, with unit-cell parameters a = 59.172, b = 65.038, c = 243.156,Å. There are two protein molecules in the asymmetric unit and the Matthews coefficient is estimated to be 2.35,Å3,Da,1, corresponding to a solvent content of 47.60%. [source] Crystallization and preliminary X-ray crystallographic studies of recombinant human betaine,homocysteine S-methyltransferaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2001Nandita Bose Betaine,homocysteine S-methyltransferase (BHMT) catalyzes a reaction essential for regulation of methionine and homocysteine metabolism and the catabolism of choline in mammalian tissues. Human recombinant BHMT (MW = 45,kDa) has been crystallized by the hanging-drop vapor-diffusion method at 294,K using ethylene glycol as the precipitant. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 109.190, b = 91.319, c = 88.661,Å, , = 122.044°, and diffract to 2.9,Å resolution on a local rotating-anode X-ray source. Rotation-function analysis and the Matthews coefficient, VM = 2.46,Å3,Da,1, are consistent with a dimer in the asymmetric unit, suggesting that the active enzyme is a tetramer with 222 symmetry. [source] Cloning, overexpression, purification, crystallization and preliminary X-ray analysis of CheY3, a response regulator that directly interacts with the flagellar `switch complex' in Vibrio choleraeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Susmita Khamrui Vibrio cholerae is the aetiological agent of the severe diarrhoeal disease cholera. This highly motile organism uses the processes of motility and chemotaxis to travel and colonize the intestinal epithelium. Chemotaxis in V. cholerae is far more complex than that in Escherichia coli or Salmonella typhimurium, with multiple paralogues of various chemotaxis genes. In contrast to the single copy of the chemotaxis response-regulator protein CheY in E. coli, V. cholerae contains four CheYs (CheY1,CheY4), of which CheY3 is primarily responsible for interacting with the flagellar motor protein FliM, which is one of the major constituents of the `switch complex' in the flagellar motor. This interaction is the key step that controls flagellar rotation in response to environmental stimuli. CheY3 has been cloned, overexpressed and purified by Ni,NTA affinity chromatography followed by gel filtration. Crystals of CheY3 were grown in space group R3, with a calculated Matthews coefficient of 2.33,Å3,Da,1 (47% solvent content) assuming the presence of one molecule per asymmetric unit. [source] Crystallization and preliminary X-ray analysis of cecropin B from Bombyx moriACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Zhongyuan Liu Cecropin B is a 37-residue cationic antimicrobial peptide derived from the haemolymph of Bombyx mori. The precise mechanism by which cecropins exert their antimicrobial and cytolytic activities is not well understood. Crystals of cecropin B were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant at 289,K. The crystal diffracted to 1.43,Å resolution using X-ray radiation and belonged to the orthorhombic space group P1, with unit-cell parameters a = 15.08, b = 22.75, c = 30.20,Å, , = 96.9, , = 103.1, , = 96.5°. The asymmetric unit contained only one molecule of cecropin B, with a calculated Matthews coefficient of 2.48,Å3,Da,1 and a solvent content of 50.4%. [source] Crystallization and preliminary X-ray crystallographic analysis of highly thermostable L2 lipase from the newly isolated Bacillus sp.ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Purified thermostable recombinant L2 lipase from Bacillus sp. L2 was crystallized by the counter-diffusion method using 20% PEG 6000, 50,mM MES pH 6.5 and 50,mM NaCl as precipitant. X-ray diffraction data were collected to 2.7,Å resolution using an in-house Bruker X8 PROTEUM single-crystal diffractometer system. The crystal belonged to the primitive orthorhombic space group P212121, with unit-cell parameters a = 87.44, b = 94.90, c = 126.46,Å. The asymmetric unit contained one single molecule of protein, with a Matthews coefficient (VM) of 2.85,Å3,Da,1 and a solvent content of 57%. [source] Purification, crystallization and preliminary X-ray analysis of apo glyceraldehyde-3-phosphate dehydrogenase 1 (GAP1) from methicillin-resistant Staphylococcus aureus (MRSA252)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Somnath Mukherjee Glyceraldehyde-3-phosphate dehydrogenase 1 (GAP1) from methicillin-resistant Staphylococcus aureus (MRSA252) has been purified to homogeneity in the apo form. The protein was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group P21, with unit-cell parameters a = 69.95, b = 93.68, c = 89.05,Å, , = 106.84°. X-ray diffraction data have been collected and processed to a maximum resolution of 2.2,Å. The presence of one tetramer in the asymmetric unit gives a Matthews coefficient (VM) of 1.81,Å3,Da,1 with a solvent content of 32%. The structure has been solved by molecular replacement and structure refinement is now in progress. [source] Crystallization and preliminary X-ray crystallographic analysis of MinE, the cell-division topological specificity factor from Helicobacter pyloriACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Gil Bu Kang Cell division in Gram-negative bacteria is driven by the formation of an FtsZ ring at the division site. MinE regulates the proper placement of the FtsZ ring at mid-cell by blocking the inhibitory action of the MinCD complex. Diffraction data were collected at 2.8,Å resolution from a native crystal of full-length Helicobacter pylori MinE. The crystal belonged to space group P64. Assuming the presence of two molecules in the asymmetric unit, the calculated Matthews coefficient was 2.58,Å3,Da,1, which corresponds to a solvent content of 52.3%. For MAD phasing, a four-wavelength data set was collected at 3.0,Å resolution. [source] Crystallization and preliminary X-ray diffraction analysis of the dimerization domain of the tumour suppressor ING4ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Simone Culurgioni Inhibitor of growth protein 4 (ING4) belongs to the ING family of tumour suppressors and is involved in chromatin remodelling, in growth arrest and, in cooperation with p53, in senescence and apoptosis. Whereas the structure and histone H3-binding properties of the C-terminal PHD domains of the ING proteins are known, no structural information is available for the N-terminal domains. This domain contains a putative oligomerization site rich in helical structure in the ING2,5 members of the family. The N-terminal domain of ING4 was overexpressed in Escherichia coli and purified to homogeneity. Crystallization experiments yielded crystals that were suitable for high-resolution X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 129.7, b = 188.3, c = 62.7,Å. The self-rotation function and the Matthews coefficient suggested the presence of three protein dimers per asymmetric unit. The crystals diffracted to a resolution of 2.3,Å using synchrotron radiation at the Swiss Light Source (SLS) and the European Synchrotron Radiation Facility (ESRF). [source] Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa AlgXACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Joel T. Weadge AlgX is a periplasmic protein required for the production of the exopolysaccharide alginate in Pseudomonas sp. and Azotobacter vinelandii. AlgX has been overexpressed and purified and diffraction-quality crystals have been grown using iterative seeding and the hanging-drop vapor-diffusion method. The crystals grew as flat plates with unit-cell parameters a = 46.4, b = 120.6, c = 86.9,Å, , = 95.7°. The crystals exhibited the symmetry of space group P21 and diffracted to a minimum d -spacing of 2.1,Å. On the basis of the Matthews coefficient (VM = 2.25,Å3,Da,1), two molecules were estimated to be present in the asymmetric unit. [source] Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei bruceiACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Yasutoshi Kido 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% completeness and an overall Rmerge of 9.5%. The TAO crystals belonged to the orthorhombic space group I222 or I212121, with unit-cell parameters a = 63.11, b = 136.44, c = 223.06,Å. Assuming the presence of two rTAO molecules in the asymmetric unit (2 × 38,kDa), the calculated Matthews coefficient (VM) was 3.2,Å3,Da,1, which corresponds to a solvent content of 61.0%. This is the first report of a crystal of the membrane-bound diiron proteins, which include AOXs. [source] Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Emmanuel Oluwadare Balogun In the bloodstream forms of human trypanosomes, glycerol kinase (GK; EC 2.7.1.30) is one of the nine glycosomally compartmentalized enzymes that are essential for energy metabolism. 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] Purification, crystallization and X-ray crystallographic analysis of Archaeoglobus fulgidus neelaredoxinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Tiago M. Bandeiras 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 tetragonal space group P41212, with unit-cell parameters a = b = 75.72, c = 185.44,Å. Cell-content analysis indicated the presence of a tetramer in the asymmetric unit, with a Matthews coefficient (VM) of 2.36,Å3,Da,1 and an estimated solvent content of 48%. The three-dimensional structure was determined by the MAD method and is currently under refinement. [source] Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of the putative SAICAR synthetase (PH0239) from Pyrococcus horikoshii OT3ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2010Kavyashree Manjunath 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. Assuming the presence of a hexamer in the asymmetric unit resulted in a Matthews coefficient (VM) of 2.3,Å3,Da,1, corresponding to a solvent content of about 46%. A detailed study of this protein will yield insights into structural stability at high temperatures and should be highly relevant to the development of antibiotics and anticancer drugs targeting the biosynthesis of purine nucleotides. [source] Crystallization and preliminary X-ray analysis of Psu, an inhibitor of the bacterial transcription terminator RhoACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2010Susmita Khamrui Psu, a coat protein from bacteriophage P4, inhibits Rho-dependent transcription termination both in vivo and in vitro. The Psu protein is ,-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] Crystallization and preliminary X-ray analysis of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Koji Nishikawa 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] Purification, crystallization and preliminary X-ray diffraction analysis of Cif, a virulence factor secreted by Pseudomonas aeruginosaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Christopher D. Bahl 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, , = 100.6°. The crystals diffracted to 2.39,Å resolution on a rotating-anode source. Based on the calculated Matthews coefficient (2.2,Å3,Da,1), it appears that the asymmetric unit contains four molecules. [source] Purification, crystallization and preliminary X-ray analysis of a deletion mutant of a major buckwheat allergenACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Yuichiro Kezuka A 16,kDa buckwheat protein (BWp16) is a major allergen responsible for immediate hypersensitivity reactions including anaphylaxis. A deletion mutant of BWp16 (rBWp16,N) 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 rBWp16,N. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 28.39, b = 31.54, c = 32.20,Å, , = 111.92, , = 108.91, , = 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] Purification, crystallization and preliminary crystallographic analysis of a thermostable endonuclease IV from Thermotoga maritimaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Ronny C. Hughes 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° data set was collected and processed, resulting in an overall Rmerge and a completeness of 9.5% and 99.3%, respectively. [source] Purification, crystallization and preliminary X-ray analysis of ,-glucosidase from Kluyveromyces marxianus NBRC1777ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Erina Yoshida The intracellular ,-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, , = 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] Cloning, purification and preliminary X-ray crystallographic analysis of a hypothetical protein, MJ0754, from Methanococcus jannaschii DSM 2661ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2009Eun Hye Lee The protein encoded by the MJ0754 gene from the archaeon Methanococcus jannaschii DSM 2661 is an unknown hypothetical protein. Two recombinant proteins, MJ0754 (residues 1,185) and MJ0754t (a truncated form of MJ0754, residues 11,185), were cloned from MJ0754, overexpressed as His-tag fusion proteins and purified. The crystals were found to grow under two different conditions and to have two different shapes. The crystal of MJ0754 belonged to space group P61, with unit-cell parameters a = b = 127.015, c = 48.929,Å, a calculated Matthews coefficient of 2.85,Å3,Da,1 and two molecules per asymmetric unit. The crystal of MJ0754t belonged to space group C2221, with unit-cell parameters a = 51.915, b = 79.122, c = 93.869,Å, a calculated Matthews coefficient of 2.41,Å3,Da,1 and one molecule per asymmetric unit. The SeMet-labelled P61 crystal diffracted to a resolution of 3.1,Å, while the native C2221 crystal diffracted to 1.3,Å resolution. [source] Crystallization and preliminary X-ray analysis of the small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Hideaki Ogata Ribonucleotide reduction, the unique step in DNA-precursor biosynthesis, involves radical-dependent redox chemistry and diverse metallo-cofactors. The metallo-cofactor (R2F) encoded by the nrdF (nucleotide reduction) gene in Corynebacterium ammoniagenes ATCC 6872 was isolated after homologous expression and a new crystal form of ribonucleotide reductase R2F was obtained. R2F was crystallized at 277,K using the vapour-diffusion method with PEG as the precipitating agent. A data set was collected to 1.36,Å resolution from a single crystal at 100,K using synchrotron radiation. The crystal belonged to space group C2, with unit-cell parameters a = 96.21, b = 87.68, c = 83.25,Å, , = 99.29°. The crystal contained two molecules per asymmetric unit, with a Matthews coefficient (VM) of 2.69,Å3,Da,1; the solvent content was estimated to be 54.3%. X-ray fluorescence spectroscopy and MAD diffraction data indicated the presence of manganese in the molecule and the absence of iron. [source] Crystallization and preliminary X-ray diffraction data of an LNA 7-mer duplex derived from a ricin aptamerACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Charlotte Förster Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as , - d -2,- O,4,- C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The ,- d -2,- O,4,- C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, which makes them of interest for stabilizing the structure of different nucleic acids. Aptamers, which are DNAs or RNAs targeted against specific ligands, are candidates for substitution with LNAs in order to increase their stability. A 7-mer helix derived from the terminal part of an aptamer that was targeted against ricin was chosen. The ricin aptamer originally consisted of natural RNA building blocks and showed high affinity in ricin binding. For future stabilization of the aptamer, the terminal helix has been constructed as an `all-locked' LNA and was successfully crystallized in order to investigate its structural properties. Optimization of crystal growth succeeded by the use of different metal salts as additives, such as CuCl2, MgCl2, MnCl2, CaCl2, CoCl2 and ZnSO4. Preliminary X-ray diffraction data were collected and processed to 2.8,Å resolution. The LNA crystallized in space group P65, with unit-cell parameters a = 50.11, b = 50.11, c = 40.72,Å. The crystals contained one LNA helix per asymmetric unit with a Matthews coefficient of 3.17,Å3,Da,1, which implies a solvent content of 70.15%. [source] Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Antheraea mylittaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Somnath Mukherjee Glyceraldehyde-3-phosphate dehydrogenase from Antheraea mylitta (AmGAPDH) was cloned in pQE30 vector, overexpressed in Escherichia coli M15 (pREP4) cells and purified to homogeneity. The protein was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group I222, with unit-cell parameters a = 85.81, b = 133.72, c = 220.37,Å. X-ray diffraction data were collected and processed to a maximum resolution of 2.2,Å. The presence of three molecules in the asymmetric unit gave a Matthews coefficient (VM) of 2.80,Å3,Da,1, with a solvent content of 56.08%. [source] Crystallization and preliminary diffraction analysis of a ,-galactosidase from Trichoderma reeseiACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Mirko Maksimainen An extracellular ,-galactosidase from Trichoderma reesei was crystallized from sodium cacodylate buffer using polyethylene glycol (PEG) as a precipant. Crystals grown by homogenous streak-seeding belonged to space group P1, with unit-cell parameters a = 67.3, b = 69.1, c = 81.5,Å, , = 109.1, , = 97.3, , = 114.5°. The crystals diffracted to 1.8,Å resolution using a rotating-anode generator and to 1.2,Å resolution using a synchrotron source. On the basis of the Matthews coefficient (VM = 3.16,Å3,Da,1), one molecule is estimated to be present in the asymmetric unit. The aim of the determination of the crystal structure is to increase the understanding of this industrially significant enzyme. [source] Crystallization and X-ray diffraction analysis of an `all-locked' nucleic acid duplex derived from a tRNASer microhelixACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Katja Behling Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called `locked nucleic acids' contain modified sugar moieties such as 2,- O,4,- C -methylene-bridged ,- d -ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA,DNA or LNA,RNA heteroduplexes has been well investigated, but the X-ray structure of an `all-locked' nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an `all-locked' nucleic acid helix, which was designed as an LNA originating from a tRNASer microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06,Å, , = 91.02°. A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9,Å resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48,Å3,Da,1 and a solvent content of 66.49% for the merged data. [source] Preliminary X-ray crystallographic analysis of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidansACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Yanfei Zhang The gene product of open reading frame AFE_1293 from Acidithiobacillus ferrooxidans ATCC 23270 is annotated as encoding a sulfide:quinone oxidoreductase, an enzyme that catalyses electron transfer from sulfide to quinone. Following overexpression in Escherichia coli, the enzyme was purified and crystallized using the hanging-drop vapour-diffusion method. The native crystals belonged to the tetragonal space group P42212, with unit-cell parameters a = b = 131.7, c = 208.8,Å, and diffracted to 2.3,Å resolution. Preliminary crystallographic analysis indicated the presence of a dimer in the asymmetric unit, with an extreme value of the Matthews coefficient (VM) of 4.53,Å3,Da,1 and a solvent content of 72.9%. [source] Crystallization and preliminary X-ray analysis of the LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Hideaki Ogata Light,oxygen,voltage (LOV) proteins play an important role in blue-light-dependent physiological processes in many organisms. The LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42 has been purified and crystallized at 277,K using the sitting-drop vapour-diffusion method with 2-ethoxyethanol as a precipitant. A data set was collected to 1.60,Å resolution from a single crystal at 100,K using synchrotron radiation. The LOV domain of YtvA crystallized in space group C2221, with unit-cell parameters a = 64.95, b = 83.76, c = 55.81,Å. The crystal structure of the LOV domain of YtvA was determined by the molecular-replacement method. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (VM) of 3.04,Å3,Da,1; the solvent content was estimated to be 59.5%. [source] | ||||||||||