[English] 日本語
![](img/lk-miru.gif)
- PDB-3hj8: Crystal structure determination of catechol 1,2-dioxygenase from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3hj8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol | ||||||
![]() | 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. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 654.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 658.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hgiSC ![]() 3hhxC ![]() 3hhyC ![]() 3hjqC ![]() 3hjsC ![]() 3hkpC ![]() 3i4vC ![]() 3i4yC ![]() 3i51C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 30725.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-4CL / |
#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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.6 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 39% PEG400, 0.1M Hepes, 0.1M magnesium chloride, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.542 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Apr 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→20 Å / Num. obs: 9161 / % possible obs: 87.7 % / Redundancy: 2.03 % / Rsym value: 0.05 / Net I/σ(I): 21.16 |
Reflection shell | Resolution: 2.37→2.4 Å / Redundancy: 1.37 % / Mean I/σ(I) obs: 2.57 / Num. measured obs: 1248 / Rsym value: 0.197 / % possible all: 79.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HGI Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.367 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 34.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
|