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Open data
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Basic information
Entry | Database: PDB / ID: 3f6j | ||||||||||||
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Title | F17a-G lectin domain with bound GlcNAc(beta1-3)Gal | ||||||||||||
![]() | F17a-G | ||||||||||||
![]() | SUGAR BINDING PROTEIN / bacterial adhesion / lectin / bacterial attachment / pathogenesis / immunoglobulin fold / Cell projection / Fimbrium | ||||||||||||
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. / de Boer, A. / Olsson, J.D.M. / Jonckheere, W. / De Kerpel, M. / De Genst, E. / Guerardel, Y. / Willaert, R. / Wyns, L. / Wuhrer, M. ...Buts, L. / de Boer, A. / Olsson, J.D.M. / Jonckheere, W. / De Kerpel, M. / De Genst, E. / Guerardel, Y. / Willaert, R. / Wyns, L. / Wuhrer, M. / Oscarson, S. / De Greve, H. / Bouckaert, J. | ||||||||||||
![]() | ![]() 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.M. / 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 | ![]() | 52.3 KB | Display | ![]() |
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PDB format | ![]() | 35.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.4 KB | Display | ![]() |
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Full document | ![]() | 772.6 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f64C ![]() 3ffoC ![]() 4bwoC ![]() 4k0oC ![]() 1o9vS 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
#1: Protein | Mass: 19048.227 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain, UNP residues 23-199 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 10%(v/v) 2-propanol, 20%(w/v) PEG 4000, 100mM HEPES, pH 7.5, vapor diffusion, 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: May 1, 2006 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8047 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 15865 / Num. obs: 15865 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Biso Wilson estimate: 17.199 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 16.88 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1366 / % possible all: 90.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O9V chain A Resolution: 1.75→32.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.54 / SU ML: 0.083 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.133 / 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 max: 44.29 Å2 / Biso mean: 17.004 Å2 / Biso min: 8.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→32.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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