[English] 日本語
Yorodumi- PDB-2q2q: Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q2q | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida | ||||||
Components | Beta-D-hydroxybutyrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Pseudomonas putida / SDR | ||||||
Function / homology | Function and homology information 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Paithankar, K.S. / Feller, C. / Kuettner, E.B. / Keim, A. / Grunow, M. / Strater, N. | ||||||
Citation | Journal: Febs J. / Year: 2007 Title: Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida. Authors: Paithankar, K.S. / Feller, C. / Kuettner, E.B. / Keim, A. / Grunow, M. / Strater, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2q2q.cif.gz | 369.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2q2q.ent.gz | 303.8 KB | Display | PDB format |
PDBx/mmJSON format | 2q2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/2q2q ftp://data.pdbj.org/pub/pdb/validation_reports/q2/2q2q | HTTPS FTP |
---|
-Related structure data
Related structure data | 2q2vC 2q2wC 1wmbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 26507.275 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: bdhA / Production host: Escherichia coli (E. coli) References: UniProt: Q9AE70, 3-hydroxybutyrate dehydrogenase #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.55 % |
---|---|
Crystal grow | Temperature: 295 K / pH: 7.1 Details: 17-20 % PEG 1500, 0.2mM calcium chloride, 10mM acetoacetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5419 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→30 Å / Num. obs: 105219 / % possible obs: 96.7 % |
Reflection shell | Resolution: 2.02→2.09 Å / Rmerge(I) obs: 0.593 / % possible all: 74.4 |
-Phasing
Phasing MR | Rfactor: 0.572 / Cor.coef. Fo:Fc: 0.297
|
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WMB Resolution: 2.02→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.117 / SU ML: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.86 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.07 Å
|