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Yorodumi- PDB-5o0s: Crystal structure of txGH116 (beta-glucosidase from Thermoanaerob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o0s | ||||||
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Title | Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with unreacted beta Cyclophellitol Cyclosulfate probe ME711 | ||||||
Components | Glucosylceramidase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoanaerobacterium xylanolyticum LX-11 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | ||||||
Authors | Wu, L. / Offen, W.A. / Breen, I.Z. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: ACS Cent Sci / Year: 2017 Title: 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor. Authors: Artola, M. / Wu, L. / Ferraz, M.J. / Kuo, C.L. / Raich, L. / Breen, I.Z. / Offen, W.A. / Codee, J.D.C. / van der Marel, G.A. / Rovira, C. / Aerts, J.M.F.G. / 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 | 5o0s.cif.gz | 354.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o0s.ent.gz | 284.9 KB | Display | PDB format |
PDBx/mmJSON format | 5o0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o0s_validation.pdf.gz | 908.6 KB | Display | wwPDB validaton report |
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Full document | 5o0s_full_validation.pdf.gz | 913.9 KB | Display | |
Data in XML | 5o0s_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 5o0s_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/5o0s ftp://data.pdbj.org/pub/pdb/validation_reports/o0/5o0s | HTTPS FTP |
-Related structure data
Related structure data | 5npbC 5npcC 5npdC 5npeC 5npfC 5fjsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 90366.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria) Gene: Thexy_2211 / Production host: Escherichia coli (E. coli) / References: UniProt: F6BL85, glucosylceramidase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-9FQ / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 100 mM MES pH 6.5 0.2 M Ammonium Sulfate 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→59.39 Å / Num. obs: 275502 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.16→1.18 Å / Redundancy: 7.5 % / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 1 / Num. unique obs: 13526 / CC1/2: 0.515 / Rpim(I) all: 1.14 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5fjs Resolution: 1.16→59.39 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.62 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.91 Å2
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Refinement step | Cycle: 1 / Resolution: 1.16→59.39 Å
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Refine LS restraints |
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