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- PDB-7dku: 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: 7dku | |||||||||
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Title | Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with cellobiose | |||||||||
![]() | 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 | ![]() | 189.8 KB | Display | ![]() |
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PDB format | ![]() | 145.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 54.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dksC ![]() 7dktC ![]() 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: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose | ||||||
#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: 44.26 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.16 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: 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: 1.6→89 Å / Num. obs: 105220 / % possible obs: 98.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 50.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Num. unique obs: 9618 / CC1/2: 0.973 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BVU Resolution: 1.6→88.63 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.285 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.079 / 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: 51.02 Å2 / Biso mean: 14.986 Å2 / Biso min: 6.08 Å2
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Refinement step | Cycle: final / Resolution: 1.6→88.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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