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- PDB-4d52: 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: 4d52 | |||||||||
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Title | CRYSTAL STRUCTURE OF FUCOSE BINDING LECTIN FROM ASPERGILLUS FUMIGATUS (AFL) IN COMPLEX WITH L-GALACTOPYRANOSE. | |||||||||
![]() | (FUCOSE-SPECIFIC LECTIN ...) x 3 | |||||||||
![]() | SUGAR BINDING PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Houser, J. / Cioci, G. / Komarek, J. / Wimmerowa, M. / Kostlanova, N. / Lahmann, M. / Varrot, A. / Imberty, A. | |||||||||
![]() | ![]() 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 | ![]() | 284 KB | Display | ![]() |
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PDB format | ![]() | 228.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 533 KB | Display | ![]() |
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Full document | ![]() | 539.9 KB | Display | |
Data in XML | ![]() | 57.3 KB | Display | |
Data in CIF | ![]() | 83.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4agtC ![]() 4ah4C ![]() 4ahaC ![]() 4c1yC ![]() 4d4uC ![]() 4uouC ![]() 4agiS C: citing same article ( S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-FUCOSE-SPECIFIC LECTIN ... , 3 types, 4 molecules ABDC
#1: Protein | Mass: 34612.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 34644.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | | Mass: 34676.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 2 types, 26 molecules ![](data/chem/img/GXL.gif)
![](data/chem/img/GIV.gif)
![](data/chem/img/GIV.gif)
#4: Sugar | ChemComp-GXL / #5: Sugar | ChemComp-GIV / |
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-Non-polymers , 6 types, 1079 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PG4 / #8: Chemical | ChemComp-ZN / | #9: Chemical | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.8 % / Description: NONE |
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Crystal grow | Details: 200 MM CACL2, 25% PEG 4K AND 100 MM TRIS, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→34.44 Å / Num. obs: 121067 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.2 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AGI Resolution: 1.76→111.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.106 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.275 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→111.82 Å
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Refine LS restraints |
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