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Yorodumi- PDB-6s3z: Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3z | |||||||||
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Title | Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Fructose 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 hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process 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 | 6s3z.cif.gz | 296.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3z.ent.gz | 239.1 KB | Display | PDB format |
PDBx/mmJSON format | 6s3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3z ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3z | HTTPS FTP |
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-Related structure data
Related structure data | 6fjeC 6fjgC 6s2gC 6s2hC 6s82C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 42 - 665 / Label seq-ID: 42 - 665
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 72007.148 Da / Num. of mol.: 2 / Mutation: D80A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaffia rhodozyma (fungus) / Gene: INV / Plasmid: PIB4 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: J7HDY4 |
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-Sugars , 5 types, 34 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 979 molecules
#6: Chemical | #7: Chemical | ChemComp-PLQ / #9: 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: 4.08 Å3/Da / Density % sol: 73.7 % / Description: Diamond-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.2 M Sodium Citrate tribasic dihydrate, then soaked in 20mM fructose plus 50 mM hydroquinone 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: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2015 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.76 Å / Num. obs: 192124 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 9418 / Rpim(I) all: 0.241 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5ann Resolution: 1.85→48.61 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.935 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / 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: 26.764 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→48.61 Å
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Refine LS restraints |
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