[English] 日本語
![](img/lk-miru.gif)
- PDB-5l9c: Crystal structure of an endoglucanase from Penicillium verruculos... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5l9c | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose | |||||||||
![]() | endoglucanase | |||||||||
![]() | HYDROLASE / endohydrolysis / cellulose | |||||||||
Function / homology | ![]() cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nemashkalov, V. / Vakhrusheva, A. / Tishchenko, S. / Gabdulkhakov, A. / Kravchenko, O. / Gusakov, A. / Sinisyn, A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose Authors: Nemashkalov, V. / Vakhrusheva, A. / Tishchenko, S. / Gabdulkhakov, A. / Kravchenko, O. / Gusakov, A. / Sinisyn, A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 282.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 225.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 59 KB | Display | |
Data in CIF | ![]() | 91.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i6sS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34645.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose #4: Sugar | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 20% polyethylene glycole 6000, 50 mM bis-tris propane pH 7.0, 7% 2 methyl-2,4,-pentanediol, 5% 2 methyl-2 propanal, 6% PEG 5000, cellobiose |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.4 Å / Num. obs: 107169 / % possible obs: 90 % / Redundancy: 1.83 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.78→1.83 Å / Rmerge(I) obs: 0.498 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5I6S Resolution: 1.85→48.398 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.19
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→48.398 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|