[English] 日本語
![](img/lk-miru.gif)
- PDB-3vio: Crystal structure of beta-glucosidase from termite Neotermes kosh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vio | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with a new glucopyranosidic product | ||||||
![]() | Beta-glucosidase | ||||||
![]() | HYDROLASE / CELLULASES / GLYCOSYL HYDROLASE | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / carbohydrate catabolic process / beta-glucosidase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeng, W.Y. / Liu, C.I. / Wang, A.H.J. | ||||||
![]() | ![]() Title: High-resolution structures of Neotermes koshunensis beta-glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates Authors: Jeng, W.Y. / Wang, N.C. / Lin, C.T. / Chang, W.J. / Liu, C.I. / Wang, A.H.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 234.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 185.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 705.6 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vifC ![]() 3vigC ![]() 3vihC ![]() 3viiC ![]() 3vijC ![]() 3vikC ![]() 3vilC ![]() 3vimC ![]() 3vinC ![]() 3vipC ![]() 3ahzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55611.492 Da / Num. of mol.: 1 / Mutation: E193D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 631 molecules ![](data/chem/img/GBE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GBE / |
---|---|
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris, 18-21% (w/v) PEG 3350, 0.1-0.25M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 25, 2011 / Details: HORIZONTAL FOCUSING MIRROR |
Radiation | Monochromator: LN2-Cooled Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→30 Å / Num. all: 181100 / Num. obs: 179748 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.1 / Num. unique all: 18046 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3AHZ Resolution: 1.12→28.2 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.781 / SU ML: 0.017 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.022 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→28.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.116→1.176 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -29.1713 Å / Origin y: 87.768 Å / Origin z: 15.6529 Å
|