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Yorodumi- PDB-3evn: CRYSTAL STRUCTURE OF putative oxidoreductase from Streptococcus a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3evn | ||||||
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Title | CRYSTAL STRUCTURE OF putative oxidoreductase from Streptococcus agalactiae 2603V/r | ||||||
Components | Oxidoreductase, Gfo/Idh/MocA family | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae serogroup V (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Malashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF putative Gfo/Idh/MocA family oxidoreductase from Streptococcus agalactiae 2603V/r Authors: Malashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3evn.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3evn.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 3evn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/3evn ftp://data.pdbj.org/pub/pdb/validation_reports/ev/3evn | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36775.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria) Strain: 2603V/R / Gene: AAM99349.1, SAG0446 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q8E1B4 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% peg8000, 0.1M na cacodylate, ph 6.5, 0.2 M calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.1 % / Av σ(I) over netI: 35.36 / Number: 270038 / Rmerge(I) obs: 0.063 / Χ2: 1.39 / D res high: 1.99 Å / D res low: 50 Å / Num. obs: 37904 / % possible obs: 79.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.99→50 Å / Num. obs: 37904 / % possible obs: 79.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.063 / Χ2: 1.389 / Net I/σ(I): 35.361 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.788 / SU B: 9.654 / SU ML: 0.139 / SU R Cruickshank DPI: 0.272 / SU Rfree: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.51 Å2 / Biso mean: 45.186 Å2 / Biso min: 21.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.997→2.048 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.0217 Å / Origin y: 32.9206 Å / Origin z: 134.7591 Å
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