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Yorodumi- PDB-7dkw: Crystal structure of TxGH116 E441G nucleophile mutant from Thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dkw | |||||||||
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Title | Crystal structure of TxGH116 E441G nucleophile mutant from Thermoanaerobacterium xylanolyticum with autocondensation products from alpha-fluoroglucoside. | |||||||||
Components | beta-glucosidase | |||||||||
Keywords | HYDROLASE / beta-glucosidase / nucleophile mutant | |||||||||
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: 1.78 Å | |||||||||
Authors | Pengthaisong, S. / Ketudat Cairns, J.R. | |||||||||
Funding support | Thailand, 2items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2021 Title: Structural basis for transglycosylation in glycoside hydrolase family GH116 glycosynthases. Authors: Pengthaisong, S. / Hua, Y. / 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 | 7dkw.cif.gz | 351.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dkw.ent.gz | 279.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkw ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkw | HTTPS FTP |
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-Related structure data
Related structure data | 7dksC 7dktC 7dkuC 7dkvC 7dkxC 7dkyC 5bvuS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 91722.117 Da / Num. of mol.: 2 / Mutation: E441G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria) Strain: LX-11 / Gene: Thexy_2211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose |
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#3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose |
-Non-polymers , 3 types, 1289 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.24 M AMMONIUM SULFATE, 20% 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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→35 Å / Num. obs: 155241 / % possible obs: 99.4 % / Redundancy: 4.8 % / CC1/2: 0.998 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.78→1.84 Å / Num. unique obs: 14662 / CC1/2: 0.823 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BVU Resolution: 1.78→35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.341 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / 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: 73.87 Å2 / Biso mean: 22.459 Å2 / Biso min: 7.22 Å2
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Refinement step | Cycle: final / Resolution: 1.78→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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