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- PDB-4agt: Crystal Structure of Fucose binding lectin from Aspergillus Fumig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4agt | |||||||||
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Title | Crystal Structure of Fucose binding lectin from Aspergillus Fumigatus (AFL) in complex with Fuc1-6GlcNAc. | |||||||||
![]() | FUCOSE-SPECIFIC LECTIN FLEA | |||||||||
![]() | SUGAR BINDING PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Houser, J. / Komarek, J. / Kostlanova, N. / Lahmann, M. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M. | |||||||||
![]() | ![]() Title: Structural Insights Into Aspergillus Fumigatus Lectin Specificity: Afl Binding Sites are Functionally Non-Equivalent Authors: Houser, J. / Komarek, J. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.9 KB | Display | ![]() |
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PDB format | ![]() | 113.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ah4C ![]() 4ahaC ![]() 4c1yC ![]() 4d4uC ![]() 4d52C ![]() 4uouC ![]() 4agiS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34612.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 12 molecules ![](data/chem/img/FUC.gif)
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-FUC / |
-Non-polymers , 2 types, 424 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NA / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.49 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.87 Å / Num. obs: 38241 / % possible obs: 88.3 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 15.838 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 80 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AGI Resolution: 2→77.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.872 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.174 / 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: 13.673 Å2
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Refinement step | Cycle: LAST / Resolution: 2→77.74 Å
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Refine LS restraints |
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