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- PDB-6s3z: Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s3z | |||||||||
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Title | Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Fructose And hydroquinone | |||||||||
![]() | Beta-fructofuranosidase![]() | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ramirez-Escudero, M. / Sanz-Aparicio, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Deciphering the molecular specificity of phenolic compounds as inhibitors or glycosyl acceptors of beta-fructofuranosidase from Xanthophyllomyces dendrorhous. Authors: Ramirez-Escudero, M. / Miguez, N. / Gimeno-Perez, M. / Ballesteros, A.O. / Fernandez-Lobato, M. / Plou, F.J. / 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 | ![]() | 296.4 KB | Display | ![]() |
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PDB format | ![]() | 239.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fjeC ![]() 6fjgC ![]() 6s2gC ![]() 6s2hC ![]() 6s82C ![]() 5annS 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 domain:
NCS domain segments: Component-ID: 0 / 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: 0 / Auth seq-ID: 42 - 665 / Label seq-ID: 42 - 665
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 72007.148 Da / Num. of mol.: 2 / Mutation: D80A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 5 types, 34 molecules ![](data/chem/img/FRU.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #5: Sugar | ![]() #8: Sugar | ChemComp-NAG / ![]() |
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-Non-polymers , 3 types, 979 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PLQ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLQ.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ![]() #7: Chemical | ChemComp-PLQ / ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 73.7 % / Description: Diamond-shaped crystals |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.2 M Sodium Citrate tribasic dihydrate, then soaked in 20mM fructose plus 50 mM hydroquinone PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2015 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→48.76 Å / Num. obs: 192124 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 9418 / Rpim(I) all: 0.241 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5ann Resolution: 1.85→48.61 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.935 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / 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: 26.764 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→48.61 Å
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Refine LS restraints |
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