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Yorodumi- PDB-5b5s: Crystal structure of a carbohydrate esterase family 3 from Talaro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b5s | |||||||||
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Title | Crystal structure of a carbohydrate esterase family 3 from Talaromyces cellulolyticus | |||||||||
Components | Acetic acid | |||||||||
Keywords | HYDROLASE / Biomass / Carbohydrate esterase / Catalytic triad / Disulfide bond / Saccharification Xylanase | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / cellulose binding / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Talaromyces cellulolyticus (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | |||||||||
Authors | Watanabe, M. / Ishikawa, K. | |||||||||
Citation | Journal: Febs Lett. / Year: 2015 Title: Crystal structure of an acetylesterase from Talaromyces cellulolyticus and the importance of a disulfide bond near the active site Authors: Watanabe, M. / Fukada, H. / Inoue, H. / Ishikawa, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b5s.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b5s.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 5b5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b5s ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 22521.418 Da / Num. of mol.: 1 / Fragment: UNP residues 21-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces cellulolyticus (fungus) / Gene: axe, TCE0_004r00149 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A8IBJ8 |
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#2: Sugar | ChemComp-BOG / |
-Non-polymers , 4 types, 186 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-SO3 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 170mM ammonium sulfate, 28% PEG 4000, 5% glycerol, 0.5% n-octyl-beta-D-glucoside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 35924 / % possible obs: 99 % / Redundancy: 6.9 % / Net I/σ(I): 2.3 |
-Processing
Software |
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Refinement | Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.034 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.296 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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