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Yorodumi- PDB-2ztu: T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ztu | ||||||
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Title | T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed 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: 2 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 | 2ztu.cif.gz | 193.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ztu.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ztu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2ztu ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2ztu | HTTPS FTP |
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-Related structure data
Related structure data | 2ztlSC 2ztmC 2ztvC 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: 26682.389 Da / Num. of mol.: 4 / Mutation: T190A 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 | #3: Chemical | #4: 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: 3.01 Å3/Da / Density % sol: 59.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16%(w/v) PEG8000, 100mM magnesium chloride, 100mM HEPES-Na buffer, pH 7.5, 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-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 21, 2008 / 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: 2→50 Å / Num. all: 86335 / Num. obs: 86335 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / Num. unique all: 7621 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2ZTL Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: maximum likelihood
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Displacement parameters | Biso mean: 34 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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