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Yorodumi- PDB-6zzs: Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zzs | ||||||
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Title | Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii complexed with NAD+ and 3-oxovalerate | ||||||
Components | 3-hydroxybutyrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / (R)-3-hydroxybutyrate dehydrogenase / short-chain dehydrogenase/reductase / mesophilic enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Machado, T.F.G. / da Silva, R.G. / Gloster, T.M. / McMahon, S.A. / Oehler, V. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Dissecting the Mechanism of ( R )-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry. Authors: Machado, T.F.G. / Purg, M. / McMahon, S.A. / Read, B.J. / Oehler, V. / Aqvist, J. / Gloster, T.M. / da Silva, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zzs.cif.gz | 307 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zzs.ent.gz | 259.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/6zzs ftp://data.pdbj.org/pub/pdb/validation_reports/zz/6zzs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27567.816 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: A7M79_09600, BGC29_06470 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A1E3M3N6 #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-QT8 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.05 Å3/Da / Density % sol: 39.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 20% (v/w) PEG 4000, 0.2 M lithium sulphate, 0.1 M phosphate/citrate |
-Data collection
Diffraction | Mean temperature: 175 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→53.16 Å / Num. obs: 116141 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.059 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.825 / Mean I/σ(I) obs: 1 / Num. unique obs: 5746 / CC1/2: 0.713 / Rpim(I) all: 0.776 / % possible all: 99.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292104382 Resolution: 1.85→53.16 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.943 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.182 / 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: 84.85 Å2 / Biso mean: 31.563 Å2 / Biso min: 7.36 Å2
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Refinement step | Cycle: final / Resolution: 1.85→53.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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