+Open data
-Basic information
Entry | Database: PDB / ID: 4ket | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SsoPox W263I | ||||||
Components | Aryldialkylphosphatase | ||||||
Keywords | HYDROLASE / (beta/alpha)8-hydrolase / lactonase | ||||||
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 Å | ||||||
Authors | Gotthard, G. / Hiblot, J. / Chabriere, E. / Elias, M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Differential Active Site Loop Conformations Mediate Promiscuous Activities in the Lactonase SsoPox. Authors: Hiblot, J. / Gotthard, G. / Elias, M. / Chabriere, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ket.cif.gz | 514.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ket.ent.gz | 441.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ket.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ket_validation.pdf.gz | 508.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ket_full_validation.pdf.gz | 534.8 KB | Display | |
Data in XML | 4ket_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 4ket_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/4ket ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4ket | HTTPS FTP |
-Related structure data
Related structure data | 4kerC 4kesC 4keuC 4kevC 4kezC 4kf1C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35584.852 Da / Num. of mol.: 4 / Mutation: W263I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: php, php SSO2522, SSO2522 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q97VT7, aryldialkylphosphatase |
---|
-Non-polymers , 7 types, 929 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CO / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM Tris-HCl, 23-25% PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.66 Å / Num. obs: 92731 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1817 / WRfactor Rwork: 0.1396 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9037 / SU B: 6.082 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1495 / SU Rfree: 0.1375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 84.99 Å2 / Biso mean: 24.1689 Å2 / Biso min: 9.54 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.66 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|