[English] 日本語
![](img/lk-miru.gif)
- PDB-5jip: Crystal structure of the Clostridium perfringens spore cortex lyt... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jip | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Clostridium perfringens spore cortex lytic enzyme SleM | ||||||
![]() | Cortical-lytic enzyme | ||||||
![]() | HYDROLASE / spore / cortex / peptidoglycan-lysin | ||||||
Function / homology | ![]() peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chirgadze, D.Y. / Christie, G. / Ustok, F.I. / Al-Riyami, B. / Stott, K. | ||||||
![]() | ![]() Title: The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination. Authors: Al-Riyami, B. / Ustok, F.I. / Stott, K. / Chirgadze, D.Y. / Christie, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 275.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 222.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 58.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jfxS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37584.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): arabinose inducible expression plasmid compatible with ligation independent cloning Production host: ![]() ![]() #2: Chemical | ChemComp-MES / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.7 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES buffer, pH 6.0, 0.25 M magnesium chloride, 16% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 5, 2014 / Details: HELIOS MX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.4 Å / Num. obs: 66317 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5 / % possible all: 98.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1JFX Resolution: 1.8→42.397 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.01
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.397 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|