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- PDB-3r3x: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3r3x | ||||||
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Title | Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Bromoacetate | ||||||
![]() | Fluoroacetate dehalogenase | ||||||
![]() | HYDROLASE / FAcD / Defluorinase / Alpha/beta Hydrolase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chan, P.W.Y. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.7 KB | Display | ![]() |
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PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3r3uC ![]() 3r3vC ![]() 3r3wC ![]() 3r3yC ![]() 3r3zC ![]() 3r40C ![]() 3r41C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: CGA009 / Gene: RPA1163 / Plasmid: p15TV-L / Production host: ![]() ![]() #2: Chemical | ChemComp-BXA / | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 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: 1.8→83.33 Å / Num. obs: 49450 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.044 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.95 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() 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: 49 Å2 / Biso mean: 14.6455 Å2 / Biso min: 2.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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