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Yorodumi- PDB-5o47: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o47 | |||||||||
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Title | Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructosyl-hydroxytyrosol | |||||||||
Components | Beta-fructofuranosidase | |||||||||
Keywords | HYDROLASE / Carbohydrates / Catalysis / Catalytic Domain / Cloning / Dimerization / Glycoside Hydrolases / Fungal Proteins / Kinetics / Substrate Specificity / beta-Fructofuranosidase / invertase / transglycosylation / polyphenol / antioxidant / hydroxityrosol | |||||||||
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: 1.91 Å | |||||||||
Authors | Ramirez-Escudero, M. / Sanz-Aparicio, J. | |||||||||
Citation | Journal: Chem.Cat.Chem / Year: 2018 Title: Fructosylation of Hydroxytyrosol by the beta-Fructofuranosidase from Xanthophyllomyces dendrorhous: Insights into the Molecular Basis of the Enzyme Specificity Authors: Ramirez-Escudero, M. / Poveda, a. / Ballesteros, A.O. / Plou, F.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o47.cif.gz | 308.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o47.ent.gz | 249.2 KB | Display | PDB format |
PDBx/mmJSON format | 5o47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o47_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 5o47_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 5o47_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 5o47_validation.cif.gz | 94.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/5o47 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o47 | HTTPS FTP |
-Related structure data
Related structure data | 5annS S: Starting model for refinement |
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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: _ / 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: _ / 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 / Production host: Komagataella pastoris (fungus) / References: UniProt: J7HDY4 |
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-Sugars , 6 types, 37 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 | ChemComp-NAG / #6: Sugar | #7: Sugar | |
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-Non-polymers , 3 types, 1405 molecules
#8: Chemical | #9: Chemical | ChemComp-EDO / #10: Water | ChemComp-HOH / | |
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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 / pH: 6.5 Details: Protein was crystallized from 1.3M Sodium Citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016 / Details: KB mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→48.98 Å / Num. obs: 175297 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.91→1.94 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5ANN Resolution: 1.91→48.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.152 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.674 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→48.98 Å
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