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Yorodumi- PDB-6s82: Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s82 | |||||||||
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Title | Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Tris-buffer molecule And hydroquinone | |||||||||
Components | Beta-fructofuranosidaseSucrase | |||||||||
Keywords | HYDROLASE / Carbohydrates / Catalysis / Catalytic Domain / Cloning / Dimerization / Glycoside Hydrolases / Fungal Proteins / Kinetics / Substrate Specificity / beta-Fructofuranosidase / invertase / transglycosylation / polyphenol / antioxidant / hydroquinone | |||||||||
Function / homology | Function and homology information sucrose alpha-glucosidase activity / sucrose catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Phaffia rhodozyma (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | |||||||||
Authors | Ramirez-Escudero, M. / Sanz-Aparicio, J. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Deciphering the molecular specificity of phenolic compounds as inhibitors or glycosyl acceptors of beta-fructofuranosidase from Xanthophyllomyces dendrorhous. Authors: Ramirez-Escudero, M. / Miguez, N. / Gimeno-Perez, M. / Ballesteros, A.O. / Fernandez-Lobato, M. / Plou, F.J. / Sanz-Aparicio, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s82.cif.gz | 309 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s82.ent.gz | 248.8 KB | Display | PDB format |
PDBx/mmJSON format | 6s82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/6s82 ftp://data.pdbj.org/pub/pdb/validation_reports/s8/6s82 | HTTPS FTP |
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-Related structure data
Related structure data | 6fjeC 6fjgC 6s2gC 6s2hC 6s3zC 5annS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 72051.164 Da / Num. of mol.: 2 / Mutation: D80A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaffia rhodozyma (fungus) / Gene: INV / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: J7HDY4 |
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-Sugars , 5 types, 31 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 1370 molecules
#6: Chemical | #7: Chemical | ChemComp-PLQ / #8: Chemical | ChemComp-EDO / #10: 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: 4.12 Å3/Da / Density % sol: 70.12 % / Description: Diamond-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.3 M Sodium Citrate tribasic dihydrate, 0.1M TRIS-HCl pH 8.5, then soaked in hidroquinone PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2016 / Details: KB mirrors |
Radiation | Monochromator: Si8111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→83.94 Å / Num. obs: 190741 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 64488 / Rpim(I) all: 0.227 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5ann Resolution: 1.85→83.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.882 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.55 Å2 / Biso mean: 26.471 Å2 / Biso min: 11.53 Å2
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Refinement step | Cycle: final / Resolution: 1.85→83.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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