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- PDB-3hkp: 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: 3hkp | ||||||
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Title | Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate | ||||||
![]() | Catechol 1,2-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / beta-sandwich / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Metal-binding | ||||||
Function / homology | ![]() : / 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 | ![]() | 73.4 KB | Display | ![]() |
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PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hgiSC ![]() 3hhxC ![]() 3hhyC ![]() 3hj8C ![]() 3hjqC ![]() 3hjsC ![]() 3i4vC ![]() 3i4yC ![]() 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
#1: Protein | Mass: 30727.029 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-DHB / |
#4: Chemical | ChemComp-6PL / ( |
#5: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE MATCHES THE GENBANK DEPOSITION WITH ACCESSION CODE CAA67941, IN WHICH ALL 280 RESIDUES ...THE SEQUENCE MATCHES THE GENBANK DEPOSITION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.92 % |
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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: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→73.72 Å / Num. obs: 20872 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3014 / Rsym value: 0.458 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3HGI Resolution: 1.85→34.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.771 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.166 / 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: 19.303 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→34.4 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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