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Yorodumi- PDB-5n6s: Thermotoga maritima family 1 Glycoside hydrolase complexed with C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n6s | ||||||
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Title | Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic | ||||||
Components | Beta-glucosidase A | ||||||
Keywords | HYDROLASE / carba-cyclophellitol / mimic | ||||||
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: 2.1 Å | ||||||
Authors | Offen, W. / Davies, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors. Authors: Beenakker, T.J.M. / Wander, D.P.A. / Offen, W.A. / Artola, M. / Raich, L. / Ferraz, M.J. / Li, K.Y. / Houben, J.H.P.M. / van Rijssel, E.R. / Hansen, T. / van der Marel, G.A. / Codee, J.D.C. ...Authors: Beenakker, T.J.M. / Wander, D.P.A. / Offen, W.A. / Artola, M. / Raich, L. / Ferraz, M.J. / Li, K.Y. / Houben, J.H.P.M. / van Rijssel, E.R. / Hansen, T. / van der Marel, G.A. / Codee, J.D.C. / Aerts, J.M.F.G. / Rovira, C. / Davies, G.J. / Overkleeft, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n6s.cif.gz | 375.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n6s.ent.gz | 302.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/5n6s ftp://data.pdbj.org/pub/pdb/validation_reports/n6/5n6s | HTTPS FTP |
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-Related structure data
Related structure data | 5n6tC 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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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: bglA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08638, beta-glucosidase |
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-Non-polymers , 8 types, 437 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-IMD / | #5: Chemical | ChemComp-8P5 / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
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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: 46.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 4000, calcium acetate, trimethylamine oxide, imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→72.92 Å / Num. obs: 109393 / % possible obs: 97.3 % / Redundancy: 2.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.076 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5304 / CC1/2: 0.755 / Rpim(I) all: 0.517 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OD0.PDB Resolution: 2.1→72.91 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.864 / SU B: 8.893 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.252 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC. THERE ARE UNMODELLED REGIONS FOR C212-213, C359-363, C372, C423-427, D233, D361-364, D425-427 and D430-432. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC. THERE ARE UNMODELLED REGIONS FOR C212-213, C359-363, C372, C423-427, D233, D361-364, D425-427 and D430-432. THE LIGAND MOLECULES IN THE PROTEIN ACTIVE SITES ARE MODELLED AS FOLLOWS: CHAIN A, IN 2 CONFORMATIONS AT OCCUPANCIES 0.6/0.4, CHAIN B, IN 1 CONFORMATION, CHAIN C, WITH THE CARBA-CYCLOPHELLITOL AND AMIDE GROUPS AT OCCUPANCY 1, AND AZIDOBUTYL GROUP AT OCCUPANCY 0.5, CHAIN D, WITH ONLY THE CARBA-CYCLOPHELLITOL AND AMIDE MOIETIES PRESENT, AT OCCUPANCY 1.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.659 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→72.91 Å
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Refine LS restraints |
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