[English] 日本語
![](img/lk-miru.gif)
- PDB-6oq5: Structure of the full-length Clostridium difficile toxin B in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6oq5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs | ||||||
![]() |
| ||||||
![]() | TOXIN / Toxin VHH | ||||||
Function / homology | ![]() host cell cytosol / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, P. / Lam, K. / Jin, R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of the full-length Clostridium difficile toxin B. Authors: Chen, P. / Lam, K.H. / Liu, Z. / Mindlin, F.A. / Chen, B. / Gutierrez, C.B. / Huang, L. / Zhang, Y. / Hamza, T. / Feng, H. / Matsui, T. / Bowen, M.E. / Perry, K. / Jin, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 550.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 437.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 608.1 KB | Display | |
Data in XML | ![]() | 99.6 KB | Display | |
Data in CIF | ![]() | 131.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oq6C ![]() 6oq7C ![]() 6oq8C ![]() 2bvlS ![]() 3peeS ![]() 3v0aS ![]() 4nc2S ![]() 4np4S ![]() 4r04S ![]() 6c0bS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 270380.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Antibody , 3 types, 3 molecules DEF
#2: Antibody | Mass: 16864.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#3: Antibody | Mass: 14678.397 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Antibody | Mass: 15300.087 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#5: Chemical | ChemComp-ZN / |
---|---|
#6: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.61 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate, 0.1M magnesium acetate, and 5% PEG 8K (final pH 5.2) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.87→48.91 Å / Num. obs: 42971 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.87→3.97 Å / Rmerge(I) obs: 1.548 / Num. unique obs: 2123 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2 Resolution: 3.87→48.91 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 81.488 / SU ML: 1.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.903
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 169.399 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.87→48.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|