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- PDB-5fkb: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fkb | |||||||||
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Title | Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with 1-Kestose | |||||||||
![]() | BETA-FRUCTOFURANOSIDASE | |||||||||
![]() | HYDROLASE / AMINO ACID SEQUENCE / CARBOHYDRATES / CATALYSIS / CATALYTIC DOMAIN / CLONING / DIMERIZATION / QUATERNARY / PICHIA PASTORIS / GLYCOSIDE HYDROLASES / FUNGAL PROTEINS / KINETICS / MOLECULAR / MOLECULAR CONFORMATION / PROTEIN CONFORMATION / PROTEIN STRUCTURE / SECONDARY / SUBSTRATE SPECIFICITY / BETA-FRUCTOFURANOSIDASE / INVERTASE / PREBIOTICS / 1-KESTOSE | |||||||||
Function / homology | ![]() sucrose alpha-glucosidase activity / sucrose catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ramirez-Escudero, M. / Sanz-Aparicio, J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.7 KB | Display | ![]() |
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PDB format | ![]() | 252.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 62.9 KB | Display | |
Data in CIF | ![]() | 98.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5annSC ![]() 5fixC ![]() 5fk7C ![]() 5fk8C ![]() 5fkcC ![]() 5fmbC ![]() 5fmcC ![]() 5fmdC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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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: 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: 40 - 663
NCS oper: (Code: given / Matrix: (-1), |
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Components
-Protein / Non-polymers , 2 types, 1643 molecules AB![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 71776.828 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Water | ChemComp-HOH / | |
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-Sugars , 6 types, 35 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-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 | #6: 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 #7: Sugar | ChemComp-NAG / |
-Details
Nonpolymer details | 1-KESTOSE, PUBCHEM ENTRY CID 440080, 0-B-D-FRUCTOFURANOSYL-2-1-B-D-FRUCTOFURANOSYL-2-1-A-D- ...1-KESTOSE, PUBCHEM ENTRY CID 440080, 0-B-D-FRUCTOFURA |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.2M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M TRIS-HCL PH 8.5, THEN SOAKED IN 30MM 1-KESTOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.78→118.92 Å / Num. obs: 213888 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5ANN Resolution: 1.78→118.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.957 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY, RESIDUES 1-41 ARE DISORDERED
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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: 26.572 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→118.92 Å
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Refine LS restraints |
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