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Yorodumi- PDB-4agt: Crystal Structure of Fucose binding lectin from Aspergillus Fumig... -
+Open data
-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. | |||||||||
Components | FUCOSE-SPECIFIC LECTIN FLEA | |||||||||
Keywords | SUGAR BINDING PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Houser, J. / Komarek, J. / Kostlanova, N. / Lahmann, M. / Cioci, G. / Varrot, A. / Imberty, A. / Wimmerova, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4agt.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4agt.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 4agt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4agt ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4agt | HTTPS FTP |
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-Related structure data
Related structure data | 4ah4C 4ahaC 4c1yC 4d4uC 4d52C 4uouC 4agiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4WW81 |
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-Sugars , 3 types, 12 molecules
#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
#4: Chemical | ChemComp-NA / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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