+Open data
-Basic information
Entry | Database: PDB / ID: 4rdy | ||||||
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Title | Crystal structure of VmoLac bound to 3-oxo-C10 AHL | ||||||
Components | Parathion hydrolase | ||||||
Keywords | HYDROLASE / lactonase / quorum sensing / aryldialkylphosphatase | ||||||
Function / homology | Function and homology information catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | ||||||
Biological species | Vulcanisaeta moutnovskia (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hiblot, J. / Bzdrenga, J. / Champion, C. / Gotthard, G. / Gonzalez, D. / Chabriere, E. / Elias, M. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Crystal structure of VmoLac, a tentative quorum quenching lactonase from the extremophilic crenarchaeon Vulcanisaeta moutnovskia. Authors: Hiblot, J. / Bzdrenga, J. / Champion, C. / Chabriere, E. / Elias, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rdy.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rdy.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rdy ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rdy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35603.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vulcanisaeta moutnovskia (archaea) / Strain: 768-28 / Gene: VMUT_2255 / Production host: Escherichia coli (E. coli) / References: UniProt: F0QXN6 |
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-Non-polymers , 5 types, 680 molecules
#2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 3.81 Å3/Da / Density % sol: 67.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: VmoLac was concentrated at 20mg/mL, 100 mM Tris, pH 8.5, 1.5 M ammonium sulphate, 12 % v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.75 Å / Num. obs: 72593 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.432 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.103 / 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: 24.079 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.75 Å
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