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- PDB-2cbv: Beta-glucosidase from Thermotoga maritima in complex with calyste... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cbv | ||||||
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Title | Beta-glucosidase from Thermotoga maritima in complex with calystegine B2 | ||||||
![]() | BETA-GLUCOSIDASE A | ||||||
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Function / homology | ![]() scopolin beta-glucosidase activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloster, T.M. / Madsen, R. / Davies, G.J. | ||||||
![]() | ![]() Title: Dissection of Conformationally Restricted Inhibitors Binding to a Beta-Glucosidase. Authors: Gloster, T.M. / Madsen, R. / Davies, G.J. #1: ![]() 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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 | ![]() | 210 KB | Display | ![]() |
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PDB format | ![]() | 166.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cbuC ![]() 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: (-0.02441, -0.99027, -0.13702), Vector ![]() |
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Components
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Compound details | HYDROLYSES | Sequence details | SEQUENCE CONTAINS THE HIS TAG FROM THE EXPRESSION VECTOR. NUMBERING IN THE CO-ORDINATES REFERS TO ...SEQUENCE CONTAINS THE HIS TAG FROM THE EXPRESSION | |
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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: ADSC CCD / Detector: CCD / Date: Sep 19, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→40 Å / Num. obs: 73572 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.37 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.81 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1OD0 Resolution: 1.95→72.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.826 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.162 / 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: 30.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→72.55 Å
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Refine LS restraints |
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