[English] 日本語
![](img/lk-miru.gif)
- PDB-5k8z: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5k8z | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 (pH 8.5) | ||||||||||||
![]() | Chlorite dismutase | ||||||||||||
![]() | OXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | Cyanothece sp. | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Puehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies. Authors: Schaffner, I. / Mlynek, G. / Flego, N. / Puhringer, D. / Libiseller-Egger, J. / Coates, L. / Hofbauer, S. / Bellei, M. / Furtmuller, P.G. / Battistuzzi, G. / Smulevich, G. / Djinovic-Carugo, K. / Obinger, C. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 464.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 390.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k90C ![]() 5k91C ![]() 5mauC ![]() 5nkuC ![]() 5nkvC ![]() 3qpiS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21830.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Cyan7425_1434 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 802 molecules ![](data/chem/img/MRD.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-OH / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2015 / Details: KB-mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→44.428 Å / Num. obs: 127776 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1482 / Net I/σ(I): 6.24 |
Reflection shell | Resolution: 1.55→1.605 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 0.89 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3QPI Resolution: 1.55→44.428 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.14 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.73 Å2 / Biso mean: 29.4213 Å2 / Biso min: 8.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→44.428 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
|