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Yorodumi- PDB-3vdr: Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vdr | |||||||||
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Title | Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+) | |||||||||
Components | D-3-hydroxybutyrate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / NAD DEPENDENT ENZYMES / KETONE BODIES | |||||||||
Function / homology | Function and homology information 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Alcaligenes faecalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Hoque, M.M. / Shimizu, S. / Juan, E.C.M. / Sato, Y. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Amano, H. / Suzuki, K. / Sekiguchi, T. ...Hoque, M.M. / Shimizu, S. / Juan, E.C.M. / Sato, Y. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Amano, H. / Suzuki, K. / Sekiguchi, T. / Tsunoda, M. / Takenaka, A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+. Authors: Hoque, M.M. / Shimizu, S. / Juan, E.C.M. / Sato, Y. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Amano, H. / Sekiguchi, T. / Tsunoda, M. / Takenaka, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vdr.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vdr.ent.gz | 172.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vdr_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 3vdr_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 3vdr_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 3vdr_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/3vdr ftp://data.pdbj.org/pub/pdb/validation_reports/vd/3vdr | HTTPS FTP |
-Related structure data
Related structure data | 2yz7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27118.943 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) References: UniProt: D0VWQ0, 3-hydroxybutyrate dehydrogenase |
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-Non-polymers , 7 types, 265 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-NAI / #6: Chemical | ChemComp-3HR / ( #7: Chemical | ChemComp-AAE / #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | NAI AND NAD ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. AAE AND 3HR ARE IN ALTERNATE ...NAI AND NAD ARE IN ALTERNATE CONFORMATI |
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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: 2.51 Å3/Da / Density % sol: 50.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG, 5MM NAD+, 200MM 3-HYDROXYBUTYRATE SODIUM SALT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2008 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 20947 / % possible obs: 91.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 9.48 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YZ7 Resolution: 3→43 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→43 Å
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.02 / % reflection obs: 94.9 % |