[English] 日本語
![](img/lk-miru.gif)
- PDB-1kho: Crystal Structure Analysis of Clostridium perfringens alpha-Toxin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kho | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP | ||||||
![]() | alpha-toxin | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Justin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K. | ||||||
![]() | ![]() Title: The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties. Authors: Justin, N. / Walker, N. / Bullifent, H.L. / Songer, G. / Bueschel, D.M. / Jost, H. / Naylor, C. / Miller, J. / Moss, D.S. / Titball, R.W. / Basak, A.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 156.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 126.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42421.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.46 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Na acetate, acetone, Na cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→30 Å / Num. all: 60799 / Num. obs: 59406 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.4→2.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.8 / % possible all: 91.3 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 97.8 % / Num. measured all: 1381901 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Lowest resolution: 2.53 Å / % possible obs: 91.3 % / Rmerge(I) obs: 0.187 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| |||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.38 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 8 % / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.88 |