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Yorodumi- PDB-3i51: Crystal structure determination of Catechol 1,2-Dioxygenase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i51 | ||||||
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Title | Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with 4,5-dichlorocatechol | ||||||
Components | Catechol 1,2-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / beta-sandwich / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Metal-binding | ||||||
Function / homology | Function and homology information chlorocatechol 1,2-dioxygenase activity / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / catechol-containing compound metabolic process / : / ferric iron binding Similarity search - Function | ||||||
Biological species | Rhodococcus opacus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Matera, I. / Ferraroni, M. / Kolomytseva, M. / Briganti, F. / Scozzafava, A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts. Authors: Matera, I. / Ferraroni, M. / Kolomytseva, M. / Golovleva, L. / Scozzafava, A. / Briganti, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i51.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i51.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 3i51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i51 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i51 | HTTPS FTP |
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-Related structure data
Related structure data | 3hgiSC 3hhxC 3hhyC 3hj8C 3hjqC 3hjsC 3hkpC 3i4vC 3i4yC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29734.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: grown on benzoate / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP / References: UniProt: P95607, catechol 1,2-dioxygenase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-45C / |
#4: Chemical | ChemComp-6PL / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 400 38%, MGCL2 0.1 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.0028 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0028 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→74.74 Å / Num. all: 23540 / Num. obs: 23540 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 29.67 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.452 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3HGI Resolution: 1.8→74.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.81 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→74.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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