[English] 日本語
![](img/lk-miru.gif)
- PDB-6t9f: CRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P FROM PENICILLIUM VERR... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6t9f | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P FROM PENICILLIUM VERRUCULOSUM | ||||||
![]() | Endoglucanase | ||||||
![]() | HYDROLASE / ENDOHYDROLYSIS / CELLULOSE | ||||||
Function / homology | Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / cellulase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: CRYSTAL STRUCTURE OF EN ENDOGLUCANASE S308P FROM PENICILLIUM VERRUCULOSUM Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 243.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 194.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 42.5 KB | Display | |
Data in CIF | ![]() | 59.1 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: 34655.840 Da / Num. of mol.: 4 / Mutation: S308P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.19 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: sodium formate, PIPES pH 7.0, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→59.75 Å / Num. obs: 198022 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.5443636046 Å2 / CC1/2: 0.992 / Net I/σ(I): 5.93 |
Reflection shell | Resolution: 2.24→2.38 Å / Num. unique obs: 8958 / CC1/2: 0.687 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5I6S Resolution: 2.24847339752→59.75 Å / SU ML: 0.36997125315 / Cross valid method: FREE R-VALUE / σ(F): 1.95835266787 / Phase error: 32.0032317018
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.5060772505 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24847339752→59.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|