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Yorodumi- PDB-2boy: Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2boy | ||||||
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Title | Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP | ||||||
Components | 3-CHLOROCATECHOL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / BETA BARREL / DIOXYGENASE | ||||||
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: 1.9 Å | ||||||
Authors | Ferraroni, M. / Solyanikova, I.P. / Kolomytseva, M.P. / Scozzafava, A. / Golovleva, L.A. / Briganti, F. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2006 Title: Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol. Authors: Ferraroni, M. / Kolomytseva, M.P. / Solyanikova, I.P. / Scozzafava, A. / Golovleva, L.A. / Briganti, F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Preliminary Crystallographic Analysis of 3-Chlorocatechol 1,2 Dioxygenase of a New Modified Ortho-Patway from the Gram Positive Rhodococcus Opacus 1Cp Grown on 2-Chlorophenol Authors: Ferraroni, M. / Ruiz Tarifa, M.Y. / Scozzafava, A. / Solyanikova, I.P. / Kolomytseva, M.P. / Golovleva, L.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 | 2boy.cif.gz | 445.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2boy.ent.gz | 366.4 KB | Display | PDB format |
PDBx/mmJSON format | 2boy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2boy ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2boy | HTTPS FTP |
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-Related structure data
Related structure data | 1s9aS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 28131.559 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) RHODOCOCCUS OPACUS (bacteria) / Strain: 1CP / References: UniProt: Q8G9L3, catechol 1,2-dioxygenase |
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-Non-polymers , 5 types, 1840 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-BHO / #4: Chemical | ChemComp-LPP / #5: Chemical | ChemComp-MG / #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: 2.59 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 296 K / pH: 7.5 Details: 15% PEG 8000, 0.3 M MAGNESIUM ACETATE, 100 MM HEPES PH 7.5, 5% GLYCEROL 296 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 16, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→84.5 Å / Num. obs: 1777980 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 1.57 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.8 / % possible all: 82.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S9A Resolution: 1.9→84.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.206 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→84.51 Å
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Refine LS restraints |
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