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Yorodumi- PDB-7w2w: Crystal structure of TxGH116 R786K mutant from Thermoanaerobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w2w | ||||||||||||||||||
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Title | Crystal structure of TxGH116 R786K mutant from Thermoanaerobacterium xylanolyticum with glucose | ||||||||||||||||||
Components | Glucosylceramidase | ||||||||||||||||||
Keywords | HYDROLASE / TxGH116 / beta-glucosidase / mutant / Thermoanaerobacterium xylanolyticum / 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 (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||||||||||||||
Authors | Huang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Jitonnom, J. / Ketudat Cairns, J.R. | ||||||||||||||||||
Funding support | Thailand, 5items
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Citation | Journal: Catalysts / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w2w.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w2w.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 7w2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/7w2w ftp://data.pdbj.org/pub/pdb/validation_reports/w2/7w2w | HTTPS FTP |
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-Related structure data
Related structure data | 7w2sC 7w2tC 7w2vC 7w2xC 5bvuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 96564.422 Da / Num. of mol.: 1 / Mutation: R786K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11) (bacteria) Strain: ATCC 49914 / DSM 7097 / LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, glucosylceramidase |
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-Sugars , 2 types, 2 molecules
#2: Sugar | ChemComp-GLC / |
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#3: Sugar | ChemComp-BGC / |
-Non-polymers , 5 types, 478 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-CA / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50.01 Å / Num. obs: 75984 / % possible obs: 98.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6616 / CC1/2: 0.708 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BVU Resolution: 1.79→50.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.379 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / 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: 74.19 Å2 / Biso mean: 22.193 Å2 / Biso min: 6.64 Å2
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Refinement step | Cycle: final / Resolution: 1.79→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.836 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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