[English] 日本語
![](img/lk-miru.gif)
- PDB-5gyj: Structure of catalytically active sortase from Clostridium difficile -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gyj | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of catalytically active sortase from Clostridium difficile | ||||||
![]() | Putative peptidase C60B, sortase B | ||||||
![]() | HYDROLASE / transpeptidase / Cys-His-Arg catalytic triad | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yin, J.-C. / Fei, C.-H. / Hsiao, Y.-Y. / Nix, J.C. / Huang, I.-H. / Wang, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural Insights into Substrate Recognition by Clostridium difficile Sortase. Authors: Yin, J.C. / Fei, C.H. / Lo, Y.C. / Hsiao, Y.Y. / Chang, J.C. / Nix, J.C. / Chang, Y.Y. / Yang, L.W. / Huang, I.H. / Wang, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 428.7 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qwzS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26189.283 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 630 / Gene: CD630_27180 / Plasmid: pMCSG7 / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.29 % / Description: cubic 0.3 micrometer in diameter |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 0.1M citric acid, pH3.5, 0.1M glycine, 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25.9 Å / Num. obs: 7031 / % possible obs: 94.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 55.74 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 45.85 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 10.4 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1QWZ Resolution: 2.801→25.851 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.73
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.1514 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→25.851 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|