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Yorodumi- PDB-3hhy: Crystal structure determination of Catechol 1,2-Dioxygenase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hhy | ||||||
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Title | Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with catechol | ||||||
Components | Catechol 1,2-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / beta-sandwich / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Metal-binding | ||||||
Function / homology | Function and homology information : / 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: 1.55 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 | 3hhy.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hhy.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 3hhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hhy_validation.pdf.gz | 673.8 KB | Display | wwPDB validaton report |
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Full document | 3hhy_full_validation.pdf.gz | 677.9 KB | Display | |
Data in XML | 3hhy_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3hhy_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/3hhy ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hhy | HTTPS FTP |
-Related structure data
Related structure data | 3hgiSC 3hhxC 3hj8C 3hjqC 3hjsC 3hkpC 3i4vC 3i4yC 3i51C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30725.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP / References: UniProt: P95607, catechol 1,2-dioxygenase |
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-Non-polymers , 6 types, 296 molecules
#2: Chemical | ChemComp-FE / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-6PL / ( | #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE SEQUENCE MATCHES THE GENBANK DEPOSITION WITH ACCESSION CODE CAA67941, IN WHICH ALL 280 RESIDUES ...THE SEQUENCE MATCHES THE GENBANK DEPOSITION |
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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: 2.01 Å3/Da / Density % sol: 38.73 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 39% PEG400, 0.1 M magnesium chloride, 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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→44.324 Å / Num. obs: 33822 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.215 Å2 / Rsym value: 0.074 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 14728 / Rsym value: 0.551 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HGI Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.324 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / 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: 27.015 Å2
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Refine analyze | Luzzati sigma a obs: 0.214 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.591 Å / Total num. of bins used: 20
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