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Yorodumi- PDB-3r3v: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r3v | ||||||
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Title | Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Fluoroacetate | ||||||
Components | Fluoroacetate dehalogenaseHaloacetate dehalogenase | ||||||
Keywords | HYDROLASE / FAcD / Defluorinase / Alpha/Beta Hydrolase | ||||||
Function / homology | Function and homology information haloacetate dehalogenase / haloacetate dehalogenase activity / epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Chan, P.W.Y. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Mapping the reaction coordinates of enzymatic defluorination. Authors: Chan, P.W. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r3v.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r3v.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 3r3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r3v ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r3v | HTTPS FTP |
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-Related structure data
Related structure data | 3r3uC 3r3wC 3r3xC 3r3yC 3r3zC 3r40C 3r41C 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: 34072.676 Da / Num. of mol.: 2 / Mutation: D110N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA1163 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NAM1, haloacetate dehalogenase #2: Chemical | ChemComp-FAH / | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-CL / #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: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15-24% PEG3350, 0.1-0.2M CaCl2 and 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→20 Å / Num. obs: 82700 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.794 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.577 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.088 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.56 Å2 / Biso mean: 15.3978 Å2 / Biso min: 3.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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