[English] 日本語
Yorodumi- PDB-3o32: Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o32 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatechol | ||||||
Components | Chlorocatechol 1,2-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / BETA BARREL | ||||||
Function / homology | Function and homology information : / catechol 1,2-dioxygenase activity / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / catechol-containing compound metabolic process / : / ferric iron binding Similarity search - Function | ||||||
Biological species | Rhodococcus opacus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å | ||||||
Authors | Ferraroni, M. / Briganti, F. / Kolomytseva, M. / Golovleva, L. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2013 Title: X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity. Authors: Ferraroni, M. / Kolomytseva, M. / Scozzafava, A. / Golovleva, L. / Briganti, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3o32.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3o32.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 3o32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o32_validation.pdf.gz | 744.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3o32_full_validation.pdf.gz | 764.2 KB | Display | |
Data in XML | 3o32_validation.xml.gz | 24 KB | Display | |
Data in CIF | 3o32_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o32 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o32 | HTTPS FTP |
-Related structure data
Related structure data | 3o5uC 3o6jC 3o6rC 1s9aS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28979.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP References: UniProt: O67987, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Chemical | #3: Chemical | ChemComp-35C / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 9 Details: ammonium sulphate, NaCl, TRIS, pH 9.0, vapor diffusion, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.992 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.79→29.501 Å / Num. obs: 19580 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 75.265 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 32.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1S9A Resolution: 2.85→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2749 / WRfactor Rwork: 0.2012 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8225 / SU B: 14.138 / SU ML: 0.284 / SU R Cruickshank DPI: 1.2612 / SU Rfree: 0.4063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.52 Å2 / Biso mean: 81.8203 Å2 / Biso min: 26.63 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.85→2.921 Å / Total num. of bins used: 20
|