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Yorodumi- PDB-3r41: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r41 | ||||||
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Title | Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His280Asn/apo | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 | 3r41.cif.gz | 273.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r41.ent.gz | 220.6 KB | Display | PDB format |
PDBx/mmJSON format | 3r41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/3r41 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/3r41 | HTTPS FTP |
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-Related structure data
Related structure data | 3r3uC 3r3vC 3r3wC 3r3xC 3r3yC 3r3zC 3r40C 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: 34049.617 Da / Num. of mol.: 2 / Mutation: H280N 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 | #3: Chemical | ChemComp-CL / #4: 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: 1.98 Å3/Da / Density % sol: 37.85 % |
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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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Date: Apr 3, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→82.78 Å / Num. obs: 238333 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.023 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.98 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→41.39 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.782 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.028 / 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: 65.57 Å2 / Biso mean: 13.0382 Å2 / Biso min: 4.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→41.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20
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