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Open data
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Basic information
Entry | Database: PDB / ID: 4xd4 | ||||||
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Title | Phosphotriesterase variant E2b | ||||||
![]() | Phosphotriesterase variant PTE-R3 | ||||||
![]() | HYDROLASE / dynamics / evolution / phosphotriesterase | ||||||
Function / homology | ![]() catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jackson, C.J. / Campbell, E. / Kaltenbach, M. / Tokuriki, N. | ||||||
![]() | ![]() Title: The role of protein dynamics in the evolution of new enzyme function. Authors: Campbell, E. / Kaltenbach, M. / Correy, G.J. / Carr, P.D. / Porebski, B.T. / Livingstone, E.K. / Afriat-Jurnou, L. / Buckle, A.M. / Weik, M. / Hollfelder, F. / Tokuriki, N. / Jackson, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.9 KB | Display | ![]() |
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PDB format | ![]() | 121.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pbeC ![]() 4pbfC ![]() 4pcnC ![]() 4pcpC ![]() 4xafC ![]() 4xagC ![]() 4xayC ![]() 4xazC ![]() 4xd3C ![]() 4xd5C ![]() 4xd6C ![]() 4gy0S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 36127.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na Cacodylate 30% 2-methane-2,4-pentanediol / PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.31 Å / Num. obs: 47027 / % possible obs: 91.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1183 / Net I/σ(I): 10.48 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8233 / Mean I/σ(I) obs: 1.87 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GY0 Resolution: 1.9→39.306 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.81 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.306 Å
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Refine LS restraints |
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LS refinement shell |
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