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Yorodumi- PDB-4n5l: Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n5l | ||||||
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Title | Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha | ||||||
Components | Acetoacetyl-CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta structure | ||||||
Function / homology | Function and homology information acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Ralstonia eutropha (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Kim, J.-E. / Kim, S. / Kim, K.-J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha Authors: Kim, J.-E. / Chang, J.H. / Kim, E.-J. / Kim, K.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n5l.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n5l.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/4n5l ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n5l | HTTPS FTP |
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-Related structure data
Related structure data | 4n5mC 4n5nC 1q7bS 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: 29399.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: phbB / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P14697, acetoacetyl-CoA reductase #2: 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: 2.42 Å3/Da / Density % sol: 49.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ethanol,citrate, lithium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→68.64 Å / Num. all: 68610 / Num. obs: 59854 / % possible obs: 87.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.051 / Net I/σ(I): 30 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q7B Resolution: 1.65→32.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.942 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.54 Å2 / Biso mean: 23.1289 Å2 / Biso min: 8.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→32.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.693 Å / Total num. of bins used: 20
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