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- PDB-2ceq: Beta-glycosidase from Sulfolobus solfataricus in complex with glu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ceq | ||||||
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Title | Beta-glycosidase from Sulfolobus solfataricus in complex with glucoimidazole | ||||||
![]() | BETA-GALACTOSIDASE | ||||||
![]() | HYDROLASE / ARCHAEON / FAMILY 1 / GLYCOSIDE HYDROLASE / GLUCOIMIDAZOLE / GLYCOSIDASE | ||||||
Function / homology | ![]() beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity / beta-glucosidase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloster, T.M. / Moracci, M. / Vasella, A. / Davies, G.J. | ||||||
![]() | ![]() Title: Structural, Kinetic, and Thermodynamic Analysis of Glucoimidazole-Derived Glycosidase Inhibitors. Authors: Gloster, T.M. / Roberts, S. / Perugino, G. / Rossi, M. / Moracci, M. / Panday, N. / Terinek, M. / 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 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 | ![]() | 230.8 KB | Display | ![]() |
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PDB format | ![]() | 186.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.2 KB | Display | ![]() |
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Full document | ![]() | 486.8 KB | Display | |
Data in XML | ![]() | 46.4 KB | Display | |
Data in CIF | ![]() | 69.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cerC ![]() 2cesC ![]() 2cetC ![]() 1uwqS 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: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 5 / Auth seq-ID: 1 - 489 / Label seq-ID: 1 - 489
NCS oper: (Code: given Matrix: (-0.942, 0.034, -0.335), Vector: |
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Components
#1: Protein | Mass: 56759.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | HYDROLYSIS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 4.6 Details: 11-14 PEG 4K, 0.1 M SODIUM ACETATE, PH 4.6 0.2 AMMONIUM ACETATE, 10-13 MG/ML PROTEIN 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: Apr 17, 2004 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 83599 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.94 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UWQ Resolution: 2.14→145.86 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.243 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.159 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→145.86 Å
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Refine LS restraints |
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