1OIO | pdb_00001oio

GafD (F17c-type) Fimbrial adhesin from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.238 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

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This is version 1.4 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 Biology 331: 897

  • DOI: https://doi.org/10.1016/s0022-2836(03)00841-6
  • Primary Citation Related Structures: 
    1OIO

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 39.05 kDa 
  • Atom Count: 2,980 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 356 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FIMBRIAL LECTIN
A, B
178Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q47341 (Escherichia coli)
Explore Q47341 
Go to UniProtKB:  Q47341
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47341
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.238 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.99α = 90
b = 70.47β = 104.49
c = 56.11γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Structure summary