+Open data
-Basic information
Entry | Database: PDB / ID: 2ztm | ||||||
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Title | T190S mutant of D-3-hydroxybutyrate dehydrogenase | ||||||
Components | D(-)-3-hydroxybutyrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / short chain dehydrogenase redactase / 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: 2.3 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 | 2ztm.cif.gz | 196.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ztm.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ztm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2ztm ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2ztm | HTTPS FTP |
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-Related structure data
Related structure data | 2ztlSC 2ztuC 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: 26698.389 Da / Num. of mol.: 4 / Mutation: T190S 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 | ChemComp-3HL / ( | #4: Chemical | #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: 3.01 Å3/Da / Density % sol: 59.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16%(w/v) PEG 8000, 10 mM 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: 2.3→50 Å / Num. all: 58373 / Num. obs: 58373 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5751 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2ZTL Resolution: 2.3→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: 42.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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