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Yorodumi- PDB-6s2b: Structure of beta-fructofuranosidase from Schwanniomyces occident... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s2b | ||||||
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Title | Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with fructosyl-erythritol | ||||||
Components | Fructofuranosidase | ||||||
Keywords | HYDROLASE / BETA-FRUCTOFURANOSIDASE / GLYCOSIDASE / CARBOHYDRATE / CARBOHYDRATE METABOLISM / POLISACCHARIDE DEGRADATION / COMPLEX / FRUCTOSYL-ERYTHRITOL / 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: 1.88 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 | 6s2b.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s2b.ent.gz | 191 KB | Display | PDB format |
PDBx/mmJSON format | 6s2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s2b_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6s2b_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6s2b_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 6s2b_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/6s2b ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s2b | HTTPS FTP |
-Related structure data
Related structure data | 6s1tC 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 , 3 types, 10 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 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 853 molecules
#5: Chemical | #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: 2.58 Å3/Da / Density % sol: 52.41 % / Description: Thick plates |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / 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 transferred to a soaking solution containing mother liquor and 66 mM ...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 transferred to a soaking solution containing mother liquor and 66 mM fructosyl-erythritol for 4 hours, and subsequently to a fresh drop 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 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: 1.88→49.33 Å / Num. obs: 98961 / % possible obs: 98.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.059 / Rrim(I) all: 0.137 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / Num. unique obs: 4791 / CC1/2: 0.773 / Rpim(I) all: 0.3 / Rrim(I) all: 0.7 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KF3 Resolution: 1.88→49.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.708 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.109 / 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: 18.584 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→49.33 Å
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Refine LS restraints |
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