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Yorodumi- PDB-5bx5: Crystal structure of Thermoanaerobacterium xylanolyticum GH116 be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bx5 | ||||||||||||
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Title | Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with glucose | ||||||||||||
Components | beta-glucosidase | ||||||||||||
Keywords | HYDROLASE / Thermoanaerobacterium xylanolyticum LX-11 / GH116 / beta-glucosidase / glucose | ||||||||||||
Function / homology | Function and homology information glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase 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: 1.85 Å | ||||||||||||
Authors | Charoenwattanasatien, R. / Pengthaisong, S. / Sansenya, S. / Mutoh, R. / Hua, Y. / Tanaka, H. / Kurisu, G. / Ketudat Cairns, J.R. | ||||||||||||
Funding support | Thailand, Japan, 3items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Bacterial beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoh, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / ...Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoh, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / Kurisu, G. / Ketudat Cairns, J.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bx5.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bx5.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/5bx5 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bx5 | HTTPS FTP |
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-Related structure data
Related structure data | 5bvuSC 5bx2C 5bx3C 5bx4C 5fjsC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 91794.180 Da / Num. of mol.: 1 / Fragment: UNP residues 19-806 Source method: isolated from a genetically manipulated source Details: The author believe that the E.C. number and the enzyme name in UniProt F6BL85 is incorrect. Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria) Strain: LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase |
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#2: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 487 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.16 M Ammonium Sulfate, 24% PEG 4000, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 66687 / % possible obs: 95.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 37.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 8.3 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BVU Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.254 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.124 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→50 Å
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