+Open data
-Basic information
Entry | Database: PDB / ID: 4xd3 | ||||||
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Title | Phosphotriesterase variant E3 | ||||||
Components | Phosphotriesterase variant PTE-E1 | ||||||
Keywords | HYDROLASE / dynamics / evolution / phosphotriesterase | ||||||
Function / homology | Function and homology information catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | ||||||
Biological species | Brevundimonas diminuta (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Jackson, C.J. / Campbell, E. / Kaltenbach, M. / Tokuriki, N. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xd3.cif.gz | 159.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xd3.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 4xd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/4xd3 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xd3 | HTTPS FTP |
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-Related structure data
Related structure data | 4pbeC 4pbfC 4pcnC 4pcpC 4xafC 4xagC 4xayC 4xazC 4xd4C 4xd5C 4xd6C 4gy0S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36141.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060GPQ5 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-MPD / ( #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: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM NaCacodylate 30% 2-methane-2,4-pentanediol / PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→39.41 Å / Num. obs: 91982 / % possible obs: 99.91 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.0828 / Net I/σ(I): 16.45 |
Reflection shell | Resolution: 1.57→1.626 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.9643 / Mean I/σ(I) obs: 2.31 / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GY0 Resolution: 1.57→39.408 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15 / 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: 1.57→39.408 Å
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Refine LS restraints |
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LS refinement shell |
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