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Open data
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Basic information
Entry | Database: PDB / ID: 4k0o | |||||||||
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Title | F17b-G lectin domain with bound GlcNAc(beta1-3)Gal | |||||||||
![]() | F17b-G fimbrial adhesin | |||||||||
![]() | SUGAR BINDING PROTEIN / immunoglobulin-like fold / lectin / carbohydrate receptor / acetylation of lysine side chain / cellular envelope | |||||||||
Function / homology | ![]() adhesion of symbiont to host / cell adhesion involved in single-species biofilm formation / pilus / carbohydrate binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Buts, L. / Loris, R. / Bouckaert, J. / Moonens, K. | |||||||||
![]() | ![]() Title: Structural Sampling of Glycan Interaction Profiles Reveals Mucosal Receptors for Fimbrial Adhesins of Enterotoxigenic Escherichia coli Authors: Lonardi, E. / Moonens, K. / Buts, L. / de Boer, A.R. / Olsson, J.D. / Weiss, M.S. / Fabre, E. / Guerardel, Y. / Deelder, A.M. / Oscarson, S. / Wuhrer, M. / Bouckaert, 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 | ![]() | 53.4 KB | Display | ![]() |
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PDB format | ![]() | 35.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 831.6 KB | Display | ![]() |
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Full document | ![]() | 834.3 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f64C ![]() 3f6jC ![]() 3ffoC ![]() 4bwoC ![]() 2bs8S 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 on special symmetry positions |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 18937.900 Da / Num. of mol.: 1 / Fragment: UNP residues 23-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-methyl beta-D-galactopyranoside Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % / Mosaicity: 0.574 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2M lithium sulphate, 10mM nickel chloride, 100mM TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 13, 2005 / Details: MANUFACTURED BY MARUSA | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DESY X13 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8128 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→99 Å / Num. all: 13775 / Num. obs: 13775 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.8 % / Rmerge(I) obs: 0.069 / Χ2: 1.013 / Net I/σ(I): 21.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BS8 Resolution: 2.15→43.823 Å / Occupancy max: 1 / Occupancy min: 0.77 / FOM work R set: 0.8033 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 26.95 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.01 Å2 / Biso mean: 54.6589 Å2 / Biso min: 34.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→43.823 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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