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Yorodumi- PDB-3vdq: Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate deh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vdq | |||||||||
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Title | Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex with NAD(+) and acetate | |||||||||
Components | D-3-hydroxybutyrate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / NAD DEPENDENT ENZYME / HYDROXYBUTYRATE DEHYDROGENASE / KETONE BODIES | |||||||||
Function / homology | Function and homology information 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | Alcaligenes faecalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Hoque, M.M. / Shimizu, S. / Hossain, M.T. / Yamamoto, T. / Suzuki, K. / Takenaka, A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD+ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family. Authors: Hoque, M.M. / Shimizu, S. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Tsunoda, M. / Amano, H. / Sekiguchi, T. / Takenaka, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vdq.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vdq.ent.gz | 177.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/3vdq ftp://data.pdbj.org/pub/pdb/validation_reports/vd/3vdq | HTTPS FTP |
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-Related structure data
Related structure data | 2yz7SC S: Starting model for refinement C: citing same article (ref.) |
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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 , 5 types, 845 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NAD / #5: Chemical | #6: 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: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2M SODIUM ACETATE TRIHYDRATE, 1.0M TRIS-HCL BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 17, 2007 / Details: mirrors |
Radiation | Monochromator: FLAT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.01 Å / Num. obs: 57443 / % possible obs: 100 % / Redundancy: 12.47 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 12.58 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 6.6 / Num. unique all: 5650 / Rsym value: 0.1304 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YZ7 Resolution: 2.2→40 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 40 Å / Luzzati sigma a obs: 0.26 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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