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Yorodumi- PDB-5fmb: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fmb | |||||||||
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Title | Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and HEPES buffer | |||||||||
Components | BETA-FRUCTOFURANOSIDASE | |||||||||
Keywords | HYDROLASE / CARBOHYDRATES / CATALYSIS / CATALYTIC DOMAIN / DIMERIZATION / QUATERNARY / PICHIA PASTORIS / GLYCOSIDE HYDROLASES / FUNGAL PROTEINS / KINETICS / MOLECULAR CONFORMATION / SUBSTRATE SPECIFICITY / BETA-FRUCTOFURANOSIDASE / INVERTASE / PREBIOTICS / FRUCTOSE / HEPES BUFFER | |||||||||
Function / homology | Function and homology information sucrose alpha-glucosidase activity / sucrose catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Xanthophyllomyces dendrorhous (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | |||||||||
Authors | Ramirez-Escudero, M. / Sanz-Aparicio, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Analysis of Beta-Fructofuranosidase from Xanthophyllomyces Dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity Authors: Ramirez-Escudero, M. / Gimeno-Perez, M. / Gonzalez, B. / Linde, D. / Merdzo, Z. / Fernandez-Lobato, M. / 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 | 5fmb.cif.gz | 304.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fmb.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fmb_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 5fmb_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5fmb_validation.xml.gz | 62 KB | Display | |
Data in CIF | 5fmb_validation.cif.gz | 94.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fmb ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fmb | HTTPS FTP |
-Related structure data
Related structure data | 5annSC 5fixC 5fk7C 5fk8C 5fkbC 5fkcC 5fmcC 5fmdC 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 oper: (Code: given / Matrix: (-1), |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 72021.180 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthophyllomyces dendrorhous (fungus) / Production host: KOMAGATAELLA PHAFFII (fungus) / Strain (production host): GS115 / References: UniProt: J7HDY4, beta-fructofuranosidase |
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-Sugars , 6 types, 35 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...beta-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 #6: Sugar | #8: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 1490 molecules
#7: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 70.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.2M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9786 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→119.07 Å / Num. obs: 174276 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5ANN Resolution: 1.91→119.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.653 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.272 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→119.07 Å
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