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- PDB-5fmd: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fmd | |||||||||
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Title | Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with nystose | |||||||||
![]() | BETA-FRUCTOFURANOSIDASE | |||||||||
![]() | HYDROLASE / CARBOHYDRATES / CATALYSIS / CATALYTIC DOMAIN / CLONING / DIMERIZATION / QUATERNARY / PICHIA PASTORIS / GLYCOSIDE HYDROLASES / FUNGAL PROTEINS / KINETICS / MOLECULAR CONFORMATION / SUBSTRATE SPECIFICITY / INVERTASE / PREBIOTICS / NYSTOSE | |||||||||
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 | ![]() | 303.4 KB | Display | ![]() |
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PDB format | ![]() | 249.2 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 | ![]() | 60.9 KB | Display | |
Data in CIF | ![]() | 93.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5annSC ![]() 5fixC ![]() 5fk7C ![]() 5fk8C ![]() 5fkbC ![]() 5fkcC ![]() 5fmbC ![]() 5fmcC 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (-1), |
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Components
-Protein / Non-polymers , 2 types, 1446 molecules AB![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 72021.180 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 | 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: Polysaccharide | #7: Sugar | ChemComp-NAG / |
-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: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.25M SODIUM CITRATE TRIBASIC DIHYDRATE, THEN SOAKED IN 50MM NYSTOSE, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014 / Details: KB MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→119.2 Å / Num. obs: 215107 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5ANN Resolution: 1.78→119.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.795 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.078 / 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: 25.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→119.2 Å
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Refine LS restraints |
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