[English] 日本語
![](img/lk-miru.gif)
- PDB-5m21: Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomon... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5m21 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 with 4-hydroxybenzoate bound | ||||||
![]() |
| ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraroni, M. / Da Vela, S. / Scozzafava, A. / Kolvenbach, B. / Corvini, P.F.X. | ||||||
![]() | ![]() Title: The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes. Authors: Ferraroni, M. / Da Vela, S. / Kolvenbach, B.A. / Corvini, P.F. / Scozzafava, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 413.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 332.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5m22C ![]() 5m26C ![]() 5m4oC ![]() 4zxaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18571.809 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Hydroquinone 1,2-dioxygenase small subunit / Source: (natural) ![]() References: UniProt: F8TW82, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Protein | Mass: 38238.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Hydroquinone 1,2-dioxygenase large subunit / Source: (natural) ![]() References: UniProt: F8TW83, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-PHB / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.44 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 / Details: 14% PEG 3350, 0.35 M MgCl2 and 0.1 M Mes |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→29.856 Å / Num. obs: 130301 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.32 % / Biso Wilson estimate: 30.103 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.86 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ZXA Resolution: 1.99→29.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.872 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Details: U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.29 Å2 / Biso mean: 27.432 Å2 / Biso min: 11.16 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.99→29.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.994→2.046 Å / Total num. of bins used: 20
|