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Yorodumi- PDB-8i5t: Crystal structure of TxGH116 D593N acid/base mutant from Thermoan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i5t | ||||||||||||
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Title | Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum with cellobiose | ||||||||||||
Components | beta-glucosidase | ||||||||||||
Keywords | HYDROLASE | ||||||||||||
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: 1.5 Å | ||||||||||||
Authors | Pengthaisong, S. / Ketudat Cairns, J.R. | ||||||||||||
Funding support | Thailand, 3items
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Citation | Journal: Acs Catalysis / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i5t.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i5t.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 8i5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i5t_validation.pdf.gz | 807.8 KB | Display | wwPDB validaton report |
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Full document | 8i5t_full_validation.pdf.gz | 812.9 KB | Display | |
Data in XML | 8i5t_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 8i5t_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/8i5t ftp://data.pdbj.org/pub/pdb/validation_reports/i5/8i5t | HTTPS FTP |
-Related structure data
Related structure data | 8i5oC 8i5pC 8i5qC 8i5rC 8i5sC 8i5uC 5bvuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 91793.195 Da / Num. of mol.: 1 / Mutation: D593A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria) Strain: LX-11 / Gene: Thexy_2211 / Plasmid: PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose |
-Non-polymers , 4 types, 632 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.18 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: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 129825 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 12670 / CC1/2: 0.758 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BVU Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.066 / 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: 56.96 Å2 / Biso mean: 18.588 Å2 / Biso min: 8.17 Å2
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Refinement step | Cycle: final / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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