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- PDB-3ahy: Crystal structure of beta-glucosidase 2 from fungus Trichoderma r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ahy | ||||||
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Title | Crystal structure of beta-glucosidase 2 from fungus Trichoderma reesei in complex with Tris | ||||||
![]() | Beta-glucosidase | ||||||
![]() | HYDROLASE / cellulases / glycosyl hydrolase / manganese enhancement | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeng, W.-Y. / Liu, C.-I. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Structural and functional analysis of three beta-glucosidases from bacterium Clostridium cellulovorans, fungus Trichoderma reesei and termite Neotermes koshunensis Authors: Jeng, W.-Y. / Wang, N.-C. / Lin, M.-H. / Lin, C.-T. / Liaw, Y.-C. / Chang, W.-J. / Liu, C.-I. / Liang, P.-H. / 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 | ![]() | 832.7 KB | Display | ![]() |
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PDB format | ![]() | 691.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.6 KB | Display | ![]() |
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Full document | ![]() | 473.4 KB | Display | |
Data in XML | ![]() | 94.8 KB | Display | |
Data in CIF | ![]() | 150.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ahxC ![]() 3ahzC ![]() 3ai0C ![]() 2e3zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53257.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-TRS / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 20-22%(w/v) PEG 3350, 0.23M MgCl2, 12.5mM sodium formate, pH 8.0, 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 9, 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→30 Å / Num. all: 217400 / Num. obs: 210766 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.5 / Num. unique all: 21633 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2E3Z Resolution: 1.63→29.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.315 / SU ML: 0.069 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.112 / 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: 14.638 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→29.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.718 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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