[English] 日本語
![](img/lk-miru.gif)
- PDB-5cxk: Crystal structure of beta carbonic anhydrase from Vibrio cholerae -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5cxk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of beta carbonic anhydrase from Vibrio cholerae | ||||||
![]() | Carbonic anhydrase | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ferraroni, M. / Supuran, C. | ||||||
![]() | ![]() Title: Crystal structure and kinetic studies of a tetrameric type II beta-carbonic anhydrase from the pathogenic bacterium Vibrio cholerae. Authors: Ferraroni, M. / Del Prete, S. / Vullo, D. / Capasso, C. / Supuran, C.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 365.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 298.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 521.6 KB | Display | |
Data in XML | ![]() | 71.8 KB | Display | |
Data in CIF | ![]() | 99.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2esfS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25198.596 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BCT / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.62 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG8000, ethylene glycol,Hepes |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→47.5 Å / Num. obs: 166608 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 28.602 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.092 / Χ2: 0.954 / Net I/σ(I): 10.82 / Num. measured all: 501239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Phasing
Phasing | Method: ![]() | ||||||
---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.527
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ESF Resolution: 1.9→47.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.1818 / FOM work R set: 0.8466 / SU B: 2.157 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0295 / SU Rfree: 0.0302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.55 Å2 / Biso mean: 22.753 Å2 / Biso min: 2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→47.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|