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- PDB-5o0s: Crystal structure of txGH116 (beta-glucosidase from Thermoanaerob... -
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Open data
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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 | ||||||
![]() | Glucosylceramidase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, L. / Offen, W.A. / Breen, I.Z. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.1 KB | Display | ![]() |
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PDB format | ![]() | 284.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 908.6 KB | Display | ![]() |
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Full document | ![]() | 913.9 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 51.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5npbC ![]() 5npcC ![]() 5npdC ![]() 5npeC ![]() 5npfC ![]() 5fjsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: Thexy_2211 / Production host: ![]() ![]() | ||||||
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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