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- PDB-5bx3: Crystal structure of Thermoanaerobacterium xylanolyticum GH116 be... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bx3 | ||||||||||||
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Title | Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with deoxynojirimycin | ||||||||||||
![]() | beta-glucosidase![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Charoenwattanasatien, R. / Pengthaisong, S. / Sansenya, S. / Mutoh, R. / Tankrathok, A. / Tanaka, H. / Kurisu, G. / Ketudat Cairns, J.R. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.7 KB | Display | ![]() |
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PDB format | ![]() | 141.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5bvuSC ![]() 5bx2C ![]() 5bx4C ![]() 5bx5C ![]() 5fjsC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 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.) ![]() Strain: LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 459 molecules ![](data/chem/img/NOJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NOJ / ![]() | ||||||
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#3: Chemical | ChemComp-GOL / ![]() #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-EDO / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.43 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.14 M Ammonium Sulfate, 21% PEG 3000, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.96→50 Å / Num. obs: 58660 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 10.2 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5BVU Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.591 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.124 / 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: 18.599 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→50 Å
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Refine LS restraints |
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