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Yorodumi- PDB-2ztv: The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ztv | ||||||
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Title | The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+ | ||||||
Components | D(-)-3-hydroxybutyrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / short chain dehydrogenase/reductase / SDR family / NAD / NADH / HBDH | ||||||
Function / homology | Function and homology information 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas fragi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Nakashima, K. / Nakajima, Y. / Ito, K. / Yoshimoto, T. | ||||||
Citation | Journal: J.Biochem. / Year: 2009 Title: Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor. Authors: Nakashima, K. / Ito, K. / Nakajima, Y. / Yamazawa, R. / Miyakawa, S. / Yoshimoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ztv.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ztv.ent.gz | 164.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ztv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2ztv ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2ztv | HTTPS FTP |
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-Related structure data
Related structure data | 2ztlSC 2ztmC 2ztuC 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
#1: Protein | Mass: 26712.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fragi (bacteria) / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue References: UniProt: Q5KST5, 3-hydroxybutyrate dehydrogenase #2: Chemical | ChemComp-NAD / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.99 Å3/Da / Density % sol: 58.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 16%(w/v) PEG 8000, 100mM magnesium chloride, 100mM HEPES-Na buffer, pH 7.4, 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-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2007 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 93683 / Num. obs: 93683 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 50.2 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 9 / Num. unique all: 9248 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2ZTL Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.63 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.141 / 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 mean: 35.248 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.001 Å / Total num. of bins used: 20
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