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- PDB-7w2v: Crystal structure of TxGH116 R786A mutant from Thermoanaerobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7w2v | ||||||||||||||||||
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Title | Crystal structure of TxGH116 R786A mutant from Thermoanaerobacterium xylanolyticum with glucose | ||||||||||||||||||
![]() | Glucosylceramidase | ||||||||||||||||||
![]() | HYDROLASE / TxGH116 / beta-glucosidase / mutant / Thermoanaerobacterium xylanolyticum / glucose | ||||||||||||||||||
Function / homology | ![]() glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Huang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Jitonnom, J. / Ketudat Cairns, J.R. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Systematic Functional and Computational Analysis of Glucose-Binding Residues in Glycoside Hydrolase Family GH116. Authors: Huang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Thinkumrob, N. / Jitonnom, J. / 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 | ![]() | 182.7 KB | Display | ![]() |
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PDB format | ![]() | 139.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7w2sC ![]() 7w2tC ![]() 7w2wC ![]() 7w2xC ![]() 5bvuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 / Sugars , 2 types, 2 molecules A![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#1: Protein | Mass: 96506.320 Da / Num. of mol.: 1 / Mutation: R786A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 49914 / DSM 7097 / LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: ![]() ![]() |
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#2: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 439 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.18 M AMMONIUM SULFATE, 22% PEG 3350, 0.1 M MES, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 73832 / % possible obs: 98.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6688 / CC1/2: 0.635 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BVU Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.617 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 68.45 Å2 / Biso mean: 23.409 Å2 / Biso min: 11.4 Å2
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Refinement step | Cycle: final / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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