1OIO

GafD (F17c-type) Fimbrial adhesin from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structural Basis of Receptor-Binding by Escherichia Coli Associated with Diarrhea and Septicemia

Merckel, M.C.Tanskanen, J.Edelman, S.Westerlund-Wikstrom, B.Korhonen, T.K.Goldman, A.

(2003) J.Mol.Biol. 331: 897


  • PubMed Abstract: 
  • GafD in Escherichia coli G (F17) fimbriae is associated with diarrheal disease, and the structure of the ligand-binding domain, GafD1-178, has been determined at 1.7A resolution in the presence of the receptor sugar N-acetyl-D-glucosamine. The overal ...

    GafD in Escherichia coli G (F17) fimbriae is associated with diarrheal disease, and the structure of the ligand-binding domain, GafD1-178, has been determined at 1.7A resolution in the presence of the receptor sugar N-acetyl-D-glucosamine. The overall fold is a beta-barrel jelly-roll fold. The ligand-binding site was identified and localized to the side of the molecule. Receptor binding is mediated by side-chain as well main-chain interactions. Ala43-Asn44, Ser116-Thr117 form the sugar acetamide specificity pocket, while Asp88 confers tight binding and Trp109 appears to position the ligand. There is a disulfide bond that rigidifies the acetamide specificity pocket. The three fimbrial lectins, GafD, FimH and PapG share similar beta-barrel folds but display different ligand-binding regions and disulfide-bond patterns. We suggest an evolutionary path for the evolution of the very diverse fimbrial lectins from a common ancestral fold.


    Organizational Affiliation

    Structural Biology and Biophysics, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIMBRIAL LECTIN
A, B
178Escherichia coliMutation(s): 0 
Gene Names: f17gG (gafD)
Find proteins for Q47341 (Escherichia coli)
Go to UniProtKB:  Q47341
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.990α = 90.00
b = 70.470β = 104.49
c = 56.110γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance