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Yorodumi- PDB-4dyv: Crystal structure of a short-chain dehydrogenase/reductase SDR fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dyv | ||||||
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Title | Crystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2 | ||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthobacter autotrophicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Phenix_autosol / Resolution: 1.8 Å | ||||||
Authors | Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. / Gizzi, A. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2 Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dyv.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dyv.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dyv ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dyv | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29104.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: ATCC BAA-1158 / Py2 / Gene: Xaut_2039 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: A7IGZ0 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na-acetate trihydrate, pH 4.6, 8% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 29, 2012 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 26195 / Num. obs: 26195 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8 / Num. unique all: 2501 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: Phenix_autosol / Resolution: 1.8→35.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.753 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.1 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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