[English] 日本語
Yorodumi- PDB-7dkt: Crystal structure of TxGH116 E441A nucleophile mutant from Thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dkt | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with alpha-glucosyl fluoride | |||||||||
Components | beta-glucosidase | |||||||||
Keywords | HYDROLASE / beta-glucosidase / nucleophile mutant | |||||||||
Function / homology | Function and homology information glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase 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: 1.65 Å | |||||||||
Authors | Pengthaisong, S. / Ketudat Cairns, J.R. | |||||||||
Funding support | Thailand, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dkt.cif.gz | 187.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dkt.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 7dkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkt ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkt | HTTPS FTP |
---|
-Related structure data
Related structure data | 7dksC 7dkuC 7dkvC 7dkwC 7dkxC 7dkyC 5bvuS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 91736.148 Da / Num. of mol.: 1 / Mutation: E441A 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 | ||||||
---|---|---|---|---|---|---|---|
#2: Sugar | ChemComp-GLF / | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.48 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.14 M AMMONIUM SULFATE, 21% PEG 3350, 0.1 M MES, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→89 Å / Num. obs: 97660 / % possible obs: 99.6 % / Redundancy: 7.5 % / CC1/2: 0.985 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 7.5 % / Num. unique obs: 4756 / CC1/2: 0.83 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BVU Resolution: 1.65→88.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.746 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 50.65 Å2 / Biso mean: 16.882 Å2 / Biso min: 7.04 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→88.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|