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Yorodumi- PDB-2ztl: Closed conformation of D-3-hydroxybutyrate dehydrogenase complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ztl | ||||||
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Title | Closed conformation of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ and L-3-hydroxybutyrate | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 2ztl.cif.gz | 221.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ztl.ent.gz | 176 KB | Display | PDB format |
PDBx/mmJSON format | 2ztl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2ztl ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2ztl | HTTPS FTP |
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-Related structure data
Related structure data | 2ztmC 2ztuC 2ztvC 1wmbS 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: 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 |
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-Non-polymers , 5 types, 847 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-3HL / ( #4: Chemical | #5: Chemical | ChemComp-GOL / | #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: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16%(w/v) PEG 8000, 100mM magnesium chloride, 100mM HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: 1.8→50 Å / Num. all: 121412 / Num. obs: 121412 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 47.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 6.4 / Num. unique all: 11952 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WMB Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.497 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / 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: 28.103 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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