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- PDB-7w2t: Crystal structure of TxGH116 E730Q mutant from Thermoanaerobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7w2t | ||||||||||||||||||
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Title | Crystal structure of TxGH116 E730Q mutant from Thermoanaerobacterium xylanolyticum with glucose | ||||||||||||||||||
![]() | Glucosylceramidase![]() | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 341.2 KB | Display | ![]() |
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PDB format | ![]() | 265.8 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 ![]() 7w2vC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 96591.445 Da / Num. of mol.: 2 / Mutation: E730Q 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: ![]() ![]() ![]() ![]() #2: Sugar | ![]() #3: Chemical | ChemComp-GOL / ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.41 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.15 M AMMONIUM SULFATE, 22% PEG 3000, 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: Feb 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→50.01 Å / Num. obs: 86926 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8325 / CC1/2: 0.814 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5BVU Resolution: 2.15→50.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.974 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.193 / 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: 95.63 Å2 / Biso mean: 32.49 Å2 / Biso min: 13.73 Å2
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Refinement step | Cycle: final / Resolution: 2.15→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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