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- PDB-5vrk: Crystal structure of SsoPox AsA6 mutant (F46L-C258A-W263M-I280T) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vrk | |||||||||
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Title | Crystal structure of SsoPox AsA6 mutant (F46L-C258A-W263M-I280T) - open form | |||||||||
![]() | Aryldialkylphosphatase | |||||||||
![]() | HYDROLASE / lactonase / phosphotriesterase / mutants / quorum sensing / organophosphate / organophosphorous / insecticides. | |||||||||
Function / homology | ![]() aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hiblot, J. / Gotthard, G. / Jacquet, P. / Daude, D. / Bergonzi, C. / Chabriere, E. / Elias, M. | |||||||||
![]() | ![]() Title: Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Authors: Jacquet, P. / Hiblot, J. / Daude, D. / Bergonzi, C. / Gotthard, G. / Armstrong, N. / Chabriere, E. / Elias, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.2 KB | Display | ![]() |
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PDB format | ![]() | 238.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.3 KB | Display | ![]() |
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Full document | ![]() | 488.3 KB | Display | |
Data in XML | ![]() | 33.6 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vriC ![]() 5vsaC ![]() 5w3uC ![]() 5w3wC ![]() 5w3zC ![]() 2vc5S C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35524.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 649 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20-30 % (w/v) PEG 8000 and 50 mM Tris-HCl buffer (pH 8) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.7 Å / Num. obs: 121915 / % possible obs: 96.1 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.07 |
Reflection shell | Resolution: 1.4→1.5 Å / Rmerge(I) obs: 0.334 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vc5 Resolution: 1.4→45.97 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.336 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 22.065 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→45.97 Å
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Refine LS restraints |
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