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- PDB-2j77: Beta-glucosidase from Thermotoga maritima in complex with deoxyno... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j77 | ||||||
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Title | Beta-glucosidase from Thermotoga maritima in complex with deoxynojirimycin | ||||||
![]() | BETA-GLUCOSIDASE A | ||||||
![]() | HYDROLASE / FAMILY 1 / INHIBITOR / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION / TRANSITION STATE MIMIC / CARBOHYDRATE METABOLISM / GLYCOSIDE HYDROLASE / CELLULOSE DEGRADATION | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloster, T.M. / Zechel, D. / Davies, G.J. | ||||||
![]() | ![]() Title: Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics. Authors: Gloster, T.M. / Meloncelli, P. / Stick, R.V. / Zechel, D. / Vasella, A. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.1 KB | Display | ![]() |
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PDB format | ![]() | 160 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2j75C ![]() 2j78C ![]() 2j79C ![]() 2j7bC ![]() 2j7cC ![]() 2j7dC ![]() 2j7eC ![]() 2j7fC ![]() 2j7gC ![]() 2j7hC ![]() 1od0S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 444 / Label seq-ID: 25 - 466
NCS oper: (Code: given Matrix: (-0.03058, -0.99157, -0.12589), Vector: |
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Components
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-446 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE CRYSTALLIZED CONTAINS A HIS TAG FROM THE EXPERSSION VECTOR. THE CO-ORDINATES ARE NUMBERED ...SEQUENCE CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 7 Details: 10 MG/ML PROTEIN. 15% PEG 4K, 0.1 M IMIDAZOLE, PH 7, 0.2 M CALCIUM ACETATE. 25% ETHYLENE GLYCOL AS CRYO. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 58779 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.42 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OD0 Resolution: 2.1→72.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.349 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.207 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→72.55 Å
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Refine LS restraints |
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