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- PDB-3vif: Crystal structure of beta-glucosidase from termite Neotermes kosh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vif | ||||||
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Title | Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with gluconolactone | ||||||
![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.4 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vigC ![]() 3vihC ![]() 3viiC ![]() 3vijC ![]() 3vikC ![]() 3vilC ![]() 3vimC ![]() 3vinC ![]() 3vioC ![]() 3vipC ![]() 3ahzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/LGC.gif)
![](data/chem/img/LGC.gif)
#1: Protein | Mass: 55625.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-LGC / |
-Non-polymers , 5 types, 713 molecules ![](data/chem/img/EPE.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)
#3: Chemical | ChemComp-EPE / | ||
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#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | ChemComp-NA / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
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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 |
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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→30 Å / Num. all: 251286 / Num. obs: 246183 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.9 / Num. unique all: 25062 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AHZ Resolution: 1→28.2 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.56 / SU ML: 0.013 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 12.344 Å2
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Refinement step | Cycle: LAST / Resolution: 1→28.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.999→1.053 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -29.0814 Å / Origin y: 87.744 Å / Origin z: 15.5711 Å
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