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- PDB-3i4y: Crystal structure determination of Catechol 1,2-Dioxygenase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i4y | ||||||
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Title | Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatechol | ||||||
![]() | Catechol 1,2-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / beta-sandwich / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Metal-binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matera, I. / Ferraroni, M. / Kolomytseva, M. / Briganti, F. / Scozzafava, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 668.7 KB | Display | ![]() |
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Full document | ![]() | 675.8 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hgiSC ![]() 3hhxC ![]() 3hhyC ![]() 3hj8C ![]() 3hjqC ![]() 3hjsC ![]() 3hkpC ![]() 3i4vC ![]() 3i51C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-35C / |
#4: Chemical | ChemComp-6PL / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.57 % |
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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: ![]() ![]() ![]() |
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: 1.85→74.7 Å / Num. all: 21143 / Num. obs: 21143 / % possible obs: 96.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2943 / Rsym value: 0.539 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HGI Resolution: 1.85→74.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.669 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.172 / 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: 34.908 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→74.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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