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Yorodumi- PDB-1uz1: Family 1 b-glucosidase from Thermotoga maritima in complex with i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uz1 | ||||||
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Title | Family 1 b-glucosidase from Thermotoga maritima in complex with isofagomine lactam | ||||||
Components | BETA-GLUCOSIDASE A | ||||||
Keywords | HYDROLASE / GLUCOSIDE HYDROLYSIS / FAMILY GH1 / ENZYME / ISOFAGOMINE LACTAM | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gloster, T.M. / Macdonald, J. / Stick, R.V. / Davies, G.J. | ||||||
Citation | Journal: Chembiochem / Year: 2004 Title: Common Inhibition of Both -Glucosidases and -Mannosidases by Isofagomine Lactam Reflects Different Conformational Itineraries for Pyranoside Hydrolysis Authors: Vincent, F. / Gloster, T.M. / Macdonald, J. / Morland, C. / Stick, R.V. / Dias, F.M.V. / Prates, J.A.M. / Fontes, C.M.G.A. / Gilbert, H.J. / Davies, G.J. #1: 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 |
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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 ARE ACTUALLY 8-STRANDED BARRELS THAT ARE REPRESENTED BY 9-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uz1.cif.gz | 200.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uz1.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/1uz1 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/1uz1 | HTTPS FTP |
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-Related structure data
Related structure data | 1uz4C 1od0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 oper: (Code: given Matrix: (-0.02078, -0.99212, -0.12358), Vector: |
-Components
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CATALYTIC MODULE / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q08638, beta-glucosidase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE FULL LENGTH PROTEIN ALSO CONTAINS A HIS-TAG FROM THE PET28A CLONING VECTOR. NUMBERING OF THE ...THE FULL LENGTH PROTEIN ALSO CONTAINS A HIS-TAG FROM THE PET28A CLONING VECTOR. NUMBERING OF THE PROTEIN AGREES WITH THE UNIPROT ENTRY AND THUS IGNORES THE HIS-TAG. ANY MISSING RESIDUES/ATOMS ARE DUE TO POOR OR A LACK OF ELECTRON DENSITY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 7 Details: 10MG/ML PROTEIN IN 15% PEG 4000, 0.2 M CAAC, 0.1 M IMIDAZOLE PH7, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.065 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.065 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 65765 / % possible obs: 96 % / Redundancy: 4.95 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.34 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OD0 Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.608 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.178 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2→72.55 Å
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Refine LS restraints |
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