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- PDB-7dkt: Crystal structure of TxGH116 E441A nucleophile mutant from Thermo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dkt | |||||||||
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Title | Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with alpha-glucosyl fluoride | |||||||||
![]() | beta-glucosidase | |||||||||
![]() | HYDROLASE / beta-glucosidase / nucleophile mutant | |||||||||
Function / homology | ![]() glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pengthaisong, S. / Ketudat Cairns, J.R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.1 KB | Display | ![]() |
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PDB format | ![]() | 143.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 53.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dksC ![]() 7dkuC ![]() 7dkvC ![]() 7dkwC ![]() 7dkxC ![]() 7dkyC ![]() 5bvuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 91736.148 Da / Num. of mol.: 1 / Mutation: E441A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LX-11 / Gene: Thexy_2211 / Production host: ![]() ![]() | ||||||
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#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.48 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: 50.65 Å2 / Biso mean: 16.882 Å2 / Biso min: 7.04 Å2
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Refinement step | Cycle: final / Resolution: 1.65→88.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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