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Yorodumi- PDB-6s1t: Structure of beta-fructofuranosidase from Schwanniomyces occident... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s1t | ||||||
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Title | Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with sucrose | ||||||
Components | Fructofuranosidase | ||||||
Keywords | HYDROLASE / BETA-FRUCTOFURANOSIDASE / GLYCOSIDASE / CARBOHYDRATE / CARBOHYDRATE METABOLISM / POLISACCHARIDE DEGRADATION / COMPLEX / SUCROSE / FRUCTOSYLATION / TRANSFRUCTOSYLATION / FRUCTOOLIGOSACCHARIDES / FRUCTO-CONJUGATES | ||||||
Function / homology | Function and homology information beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / metal ion binding Similarity search - Function | ||||||
Biological species | Schwanniomyces occidentalis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Jimenez-Ortega, E. / Sanz-Aparicio, J. | ||||||
Citation | Journal: Sci Rep / Year: 2021 Title: New insights into the molecular mechanism behind mannitol and erythritol fructosylation by beta-fructofuranosidase from Schwanniomyces occidentalis. Authors: Rodrigo-Frutos, D. / Jimenez-Ortega, E. / Piedrabuena, D. / Ramirez-Escudero, M. / Miguez, N. / Plou, F.J. / Sanz-Aparicio, J. / Fernandez-Lobato, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s1t.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s1t.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 6s1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s1t_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6s1t_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6s1t_validation.xml.gz | 46.1 KB | Display | |
Data in CIF | 6s1t_validation.cif.gz | 67.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1t ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1t | HTTPS FTP |
-Related structure data
Related structure data | 6s2bC 3kf3S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 535 / Label seq-ID: 24 - 535
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61088.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schwanniomyces occidentalis (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): Y02321 / References: UniProt: E5D0X5, beta-fructofuranosidase |
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-Sugars , 4 types, 12 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 | #5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 789 molecules
#6: Chemical | #7: Chemical | ChemComp-ZN / | #8: 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: 2.63 Å3/Da / Density % sol: 53.24 % / Description: Thick plates |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 6000, 0.2 M MgCl2, and 0.1 M HEPES pH 7.0, by mixing 1 uL of protein with 0.5 uL of mother liquor. Crystals were soaked in mother liquor supplemented with 83 mM fructosyl-manitol, ...Details: 20% PEG 6000, 0.2 M MgCl2, and 0.1 M HEPES pH 7.0, by mixing 1 uL of protein with 0.5 uL of mother liquor. Crystals were soaked in mother liquor supplemented with 83 mM fructosyl-manitol, contaminated with sucrose. Cryoprotectant mother liquor supplemented with 25% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2016 / Details: KB focusing mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→49.74 Å / Num. obs: 74544 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.07 / Rrim(I) all: 0.156 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.09→2.13 Å / Redundancy: 5 % / Rmerge(I) obs: 0.569 / Num. unique obs: 4621 / CC1/2: 0.802 / Rpim(I) all: 0.286 / Rrim(I) all: 0.64 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KF3 Resolution: 2.09→49.74 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.075 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.165 / 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: 19.547 Å2
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Refinement step | Cycle: 1 / Resolution: 2.09→49.74 Å
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Refine LS restraints |
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