+Open data
-Basic information
Entry | Database: PDB / ID: 4k0o | |||||||||
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Title | F17b-G lectin domain with bound GlcNAc(beta1-3)Gal | |||||||||
Components | F17b-G fimbrial adhesin | |||||||||
Keywords | SUGAR BINDING PROTEIN / immunoglobulin-like fold / lectin / carbohydrate receptor / acetylation of lysine side chain / cellular envelope | |||||||||
Function / homology | Function and homology information adhesion of symbiont to host / cell adhesion involved in single-species biofilm formation / pilus / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Buts, L. / Loris, R. / Bouckaert, J. / Moonens, K. | |||||||||
Citation | Journal: Biology (Basel) / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k0o.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k0o.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 4k0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/4k0o ftp://data.pdbj.org/pub/pdb/validation_reports/k0/4k0o | HTTPS FTP |
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-Related structure data
Related structure data | 3f64C 3f6jC 3ffoC 4bwoC 2bs8S 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 on special symmetry positions |
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Details | biological unit is the same as asym. |
-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.) Escherichia coli (E. coli) / Gene: f17bG, F17G / Production host: Escherichia coli (E. coli) / References: UniProt: Q47200 | ||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8128 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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