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- PDB-3f64: F17a-G lectin domain with bound GlcNAc(beta1-O)paranitrophenyl ligand -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f64 | ||||||
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Title | F17a-G lectin domain with bound GlcNAc(beta1-O)paranitrophenyl ligand | ||||||
![]() | F17a-G | ||||||
![]() | SUGAR BINDING PROTEIN / Bacterial adhesin / 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. / 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 | ![]() | 51 KB | Display | ![]() |
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PDB format | ![]() | 35 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.4 KB | Display | ![]() |
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Full document | ![]() | 726.7 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f6jC ![]() 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: Sugar | ChemComp-LEC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% 2-propanol, 20% PEG 4000, 100mM HEPES, pH7.5, 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: Oct 1, 2005 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 12042 / Num. obs: 12042 / % possible obs: 94.4 % / Redundancy: 14.7 % / Biso Wilson estimate: 19.008 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 10.2 / Num. unique all: 1105 / % possible all: 91.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O9V Resolution: 1.95→48.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.965 / SU ML: 0.115 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.181 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.376 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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