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- PDB-8i5r: Crystal structure of TxGH116 D593N acid/base mutant from Thermoan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i5r | ||||||||||||
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Title | Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum | ||||||||||||
![]() | beta-glucosidase | ||||||||||||
![]() | HYDROLASE | ||||||||||||
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: Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. Authors: Pengthaisong, S. / Piniello, B. / Davies, G.J. / Rovira, C. / 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 | ![]() | 187.4 KB | Display | ![]() |
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PDB format | ![]() | 143.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i5oC ![]() 8i5pC ![]() 8i5qC ![]() 8i5sC ![]() 8i5tC ![]() 8i5uC ![]() 5bvuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 91793.195 Da / Num. of mol.: 1 / Mutation: D593A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LX-11 / Gene: Thexy_2211 / Plasmid: PET30A / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.18 M AMMONIUM SULFATE, 24% 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: Mar 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→35 Å / Num. obs: 95596 / % possible obs: 98.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.65→1.71 Å / Mean I/σ(I) obs: 4.9 / Num. unique obs: 8719 / CC1/2: 0.943 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BVU Resolution: 1.65→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.573 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / 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: 64.21 Å2 / Biso mean: 20.819 Å2 / Biso min: 9.21 Å2
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Refinement step | Cycle: final / Resolution: 1.65→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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