[English] 日本語
![](img/lk-miru.gif)
- PDB-3vih: Crystal structure of beta-glucosidase from termite Neotermes kosh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vih | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with glycerol | ||||||
![]() | 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 | ![]() | 234.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 186.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3vifC ![]() 3vigC ![]() 3viiC ![]() 3vijC ![]() 3vikC ![]() 3vilC ![]() 3vimC ![]() 3vinC ![]() 3vioC ![]() 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
#1: Protein | Mass: 55625.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
---|---|
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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2009 / Details: mirrors |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→30 Å / Num. all: 232211 / Num. obs: 224739 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.03→1.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.3 / Num. unique all: 23155 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3AHZ Resolution: 1.03→28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.649 / SU ML: 0.015 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.026 / 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: 13.751 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.03→1.086 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -29.2177 Å / Origin y: 87.8296 Å / Origin z: 15.5986 Å
|