[English] 日本語
Yorodumi- PDB-2j7f: Beta-glucosidase from Thermotoga maritima in complex with carboxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j7f | ||||||
---|---|---|---|---|---|---|---|
Title | Beta-glucosidase from Thermotoga maritima in complex with carboxylate- substituted glucoimidazole | ||||||
Components | BETA-GLUCOSIDASE A | ||||||
Keywords | HYDROLASE / FAMILY 1 / INHIBITOR / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION / TRANSITION STATE MIMIC / CARBOHYDRATE METABOLISM / GLYCOSIDE HYDROLASE / CELLULOSE DEGRADATION | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Gloster, T.M. / Zechel, D. / Vasella, A. / Davies, G.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 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 |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2j7f.cif.gz | 200.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2j7f.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j7f_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2j7f_full_validation.pdf.gz | 478.9 KB | Display | |
Data in XML | 2j7f_validation.xml.gz | 37 KB | Display | |
Data in CIF | 2j7f_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7f ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7f | HTTPS FTP |
-Related structure data
Related structure data | 2j75C 2j77C 2j78C 2j79C 2j7bC 2j7cC 2j7dC 2j7eC 2j7gC 2j7hC 1od0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
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: (-0.00261, -0.99075, -0.13566), Vector: |
-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.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q08638, beta-glucosidase #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE CRYSTALLIZED CONTAINS A HIS TAG FROM THE EXPRESSION VECTOR. THE CO-ORDINATES ARE NUMBERED ...SEQUENCE CRYSTALLIZ | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
---|---|
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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 12, 2005 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 45866 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.19 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.47 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OD0 Resolution: 2.28→72.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.9 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 33.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→72.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|