[English] 日本語
![](img/lk-miru.gif)
- PDB-7c6d: Crystal structure of E19A mutant chitosanase from Bacillus subtil... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7c6d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E19A mutant chitosanase from Bacillus subtilis MY002 complexed with 6 GlcN. | ||||||
![]() | Chitosanase | ||||||
![]() | HYDROLASE / chitosanase | ||||||
Function / homology | ![]() chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gou, Y. / Liu, Z.C. / Xie, T. / Wang, G.G. | ||||||
![]() | ![]() Title: Structure-based rational design of chitosanase CsnMY002 for high yields of chitobiose. Authors: Li, Y. / Gou, Y. / Liu, Z. / Xie, T. / Wang, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 120.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 639.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 639.2 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c6cSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27405.547 Da / Num. of mol.: 1 / Mutation: E19A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: csn, BSU26890 / Production host: ![]() ![]() |
---|---|
#2: Polysaccharide | 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.42 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 0.2M ammonium sulfate and 25%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→24.98 Å / Num. obs: 51501 / % possible obs: 98.7 % / Redundancy: 12 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 47.2 |
Reflection shell | Resolution: 1.45→1.48 Å / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 0.147 / Num. unique obs: 2256 / CC1/2: 0.986 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7C6C Resolution: 1.451→24.978 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 13.42 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.84 Å2 / Biso mean: 16.2764 Å2 / Biso min: 8.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.451→24.978 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|