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Yorodumi- PDB-4xay: Cycles of destabilization and repair underlie evolutionary transi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xay | ||||||
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Title | Cycles of destabilization and repair underlie evolutionary transitions in enzymes | ||||||
Components | Phosphotriesterase variant PTE-R8 | ||||||
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: 1.84 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 | 4xay.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xay.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xay_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 4xay_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 4xay_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4xay_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xay ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xay | HTTPS FTP |
-Related structure data
Related structure data | 4pbeC 4pbfC 4pcnC 4pcpC 4xafC 4xagC 4xazC 4xd3C 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
#1: Protein | Mass: 36049.203 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: A0A060GTM7 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MPD / ( | #4: Chemical | ChemComp-CAC / | #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: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na Cacodylate, 30% 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: 1.84→38.41 Å / Num. obs: 57480 / % possible obs: 99.95 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.1069 / Net I/σ(I): 16.17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GY0 Resolution: 1.84→38.41 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.16 / 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: 1.84→38.41 Å
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Refine LS restraints |
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LS refinement shell |
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