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Open data
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Basic information
Entry | Database: PDB / ID: 1oim | ||||||
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Title | Family 1 b-glucosidase from Thermotoga maritima | ||||||
![]() | BETA-GLUCOSIDASE A | ||||||
![]() | HYDROLASE / GLUCOSIDE HYDROLYSIS / FAMILY GH1 / ENZYME / DEOXYNOJIRIMYCIN | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloster, T. / Zechel, D.L. / Boraston, A.B. / Boraston, C.M. / Macdonald, J.M. / Tilbrook, D.M. / Stick, R.V. / Davies, G.J. | ||||||
![]() | ![]() Title: Iminosugar Glycosidase Inhibitors: Structural and Thermodynamic Dissection of the Binding of Isofagomine and 1-Deoxynojirimycin to Beta-Glucosidases Authors: Zechel, D.L. / Boraston, A.B. / Gloster, T. / Boraston, C.M. / Macdonald, J.M. / Tilbrook, D.M. / Stick, R.V. / 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 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 | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | 156.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 465.2 KB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1od0SC ![]() 1oifC ![]() 1oinC 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:
NCS oper: (Code: given Matrix: (0.99952, -0.02596, 0.01718), 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: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: RELEASE OF BETA-D-GLUCOSE DURING HYDROLYSIS OF TERMINAL, NON-REDUCING BETA-D- ...CATALYTIC ACTIVITY: RELEASE OF BETA-D-GLUCOSE DURING HYDROLYSIS | Sequence details | A1,2,233 B213,307 POOR OR MISSING DENSITY THE FULL LENGTH PROTEIN ALSO CONTAINS A HIS-TAG FROM THE ...A1,2,233 B213,307 POOR OR MISSING DENSITY THE FULL LENGTH PROTEIN ALSO CONTAINS A HIS-TAG FROM THE PET28A CLONING VECTOR. NUMBERING OF THE PROTEIN AGREES WITH THE SWISSPROT ENTRY AND IGNORES THE HIS-TAG | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING ENTRY | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 10MG/ML PROTEIN IN 15% PEG 4K, 0.2 M CAAC, 0.1M IMIDAZOLE PH7, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9392 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 207372 / % possible obs: 99.5 % / Redundancy: 3.73 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.82 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.85 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2.15 Å / Lowest resolution: 20 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 98.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OD0 Resolution: 2.15→72.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.663 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→72.55 Å
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Refine LS restraints |
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