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Yorodumi- PDB-2vc7: Structural basis for natural lactonase and promiscuous phosphotri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vc7 | ||||||||||||
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Title | Structural basis for natural lactonase and promiscuous phosphotriesterase activities | ||||||||||||
Components | ARYLDIALKYLPHOSPHATASE | ||||||||||||
Keywords | HYDROLASE / PHOSPHOTRIESTERASE / PROMISCUOUS ACTIVITIES / ENZYME EVOLUTION / HYPERTHERMOPHILIC / LACTONASE / BIOTECHNOLOGY / QUORUM SENSING | ||||||||||||
Function / homology | Function and homology information aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | Elias, M. / Dupuy, J. / Merone, L. / Mandrich, L. / Moniot, S. / Rochu, D. / Lecomte, C. / Rossi, M. / Masson, P. / Manco, G. / Chabriere, E. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural Basis for Natural Lactonase and Promiscuous Phosphotriesterase Activities. Authors: Elias, M. / Dupuy, J. / Merone, L. / Mandrich, L. / Porzio, E. / Moniot, S. / Rochu, D. / Lecomte, C. / Rossi, M. / Masson, P. / Manco, G. / Chabriere, E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vc7.cif.gz | 292.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vc7.ent.gz | 239 KB | Display | PDB format |
PDBx/mmJSON format | 2vc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vc7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2vc7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2vc7_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 2vc7_validation.cif.gz | 83.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/2vc7 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/2vc7 | HTTPS FTP |
-Related structure data
Related structure data | 2vc5SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35657.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97VT7, aryldialkylphosphatase |
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-Non-polymers , 6 types, 825 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CO / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-HT5 / ( #7: 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: 2.5 Å3/Da / Density % sol: 40.88 % / Description: NONE |
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Crystal grow | pH: 8 / Details: TRIS-HCL 50MM PH 8, 15-18% W/V PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→61.66 Å / Num. obs: 141906 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.25 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.66 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 7.1 % / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VC5 Resolution: 2.05→61.66 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.337 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BINDING OF THE LACTONE MIMIC DESCRIBED IN THE ARTICLE IS FROM MONOMER C.
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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: 28.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→61.66 Å
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Refine LS restraints |
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