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- PDB-8i5p: Crystal structure of TxGH116 D593A acid/base mutant from Thermoan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i5p | ||||||||||||
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Title | Crystal structure of TxGH116 D593A acid/base mutant from Thermoanaerobacterium xylanolyticum with cellobiose | ||||||||||||
![]() | beta-glucosidase![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 322.9 KB | Display | ![]() |
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PDB format | ![]() | 255.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8i5oC ![]() 8i5qC ![]() 8i5rC ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | ![]() Mass: 91750.172 Da / Num. of mol.: 2 / Mutation: D593A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LX-11 / Gene: Thexy_2211 / Plasmid: PET30A / Production host: ![]() ![]() ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 4 types, 307 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / ![]() | ||||
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#4: Chemical | #5: Chemical | ChemComp-MES / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.24 M AMMONIUM SULFATE, 22% 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: Oct 19, 2016 |
Radiation | Monochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.35→40 Å / Num. obs: 72545 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7146 / CC1/2: 0.75 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5BVU Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.247 / 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: 107.42 Å2 / Biso mean: 41.714 Å2 / Biso min: 19.85 Å2
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Refinement step | Cycle: final / Resolution: 2.35→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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