+Open data
-Basic information
Entry | Database: PDB / ID: 4ob7 | ||||||
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Title | Crystal structure of esterase rPPE mutant W187H | ||||||
Components | Alpha/beta hydrolase fold-3 domain protein | ||||||
Keywords | HYDROLASE / A/B HYDROLASE FOLD / Esterase / HSL-like family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas (RNA similarity group I) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Dou, S. / Kong, X.D. / Ma, B.D. / Xu, J.H. / Zhou, J.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Crystal structures of Pseudomonas putida esterase reveal the functional role of residues 187 and 287 in substrate binding and chiral recognition Authors: Dou, S. / Kong, X.D. / Ma, B.D. / Chen, Q. / Zhang, J. / Zhou, J.H. / Xu, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ob7.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ob7.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ob7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ob7_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 4ob7_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 4ob7_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4ob7_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4ob7 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4ob7 | HTTPS FTP |
-Related structure data
Related structure data | 4ob6C 4ob8C 4ou4C 4ou5C 2yh2S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36829.602 Da / Num. of mol.: 1 / Mutation: W187H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: ECU1011 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: L7PYQ2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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#2: Chemical | ChemComp-MPD / ( |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Sequence details | AUTHOR STATED THE SEQUENCE DATABASE WAS WRONG AT THIS POSITION. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % / Mosaicity: 0.573 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes/Mops-Na, pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M MgCl2, 0.03M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: VARIMAX-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→41.962 Å / Num. obs: 49350 / % possible obs: 99.5 % / Redundancy: 15.4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.04 / Net I/σ(I): 16.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YH2 Resolution: 1.65→41.962 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.9065 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 15.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.96 Å2 / Biso mean: 22.079 Å2 / Biso min: 13.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→41.962 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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