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Yorodumi- PDB-3v2h: The crystal structure of D-beta-hydroxybutyrate dehydrogenase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v2h | ||||||
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Title | The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti | ||||||
Components | D-beta-hydroxybutyrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti Authors: Zhang, Z. / 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 | 3v2h.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v2h.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 3v2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/3v2h ftp://data.pdbj.org/pub/pdb/validation_reports/v2/3v2h | HTTPS FTP |
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-Related structure data
Related structure data | 1wmbS S: Starting model for refinement |
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Similar structure data | |
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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4 |
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Unit cell |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 30413.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: bdhA, RB1136, SMb21010 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: O86034, 3-hydroxybutyrate dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH5.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 13005 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 55.25 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 13 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1268 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WMB Resolution: 3→44.583 Å / SU ML: 0.46 / Isotropic thermal model: Isotropic / σ(F): 0.15 / Phase error: 24.55 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.611 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→44.583 Å
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Refine LS restraints |
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LS refinement shell |
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