1MFE

RECOGNITION OF A CELL-SURFACE OLIGO-SACCHARIDE OF PATHOGENIC SALMONELLA BY AN ANTIBODY FAB FRAGMENT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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This is version 3.0 of the entry. See complete history. 


Literature

Recognition of a cell-surface oligosaccharide of pathogenic Salmonella by an antibody Fab fragment.

Cygler, M., Rose, D.R., Bundle, D.R.

(1991) Science 253: 442-445

  • DOI: https://doi.org/10.1126/science.1713710
  • Primary Citation of Related Structures:  
    1MFE

  • PubMed Abstract: 

    The 2.05 angstrom (A) resolution crystal structure of a dodecasaccharide-Fab complex revealed an unusual carbohydrate recognition site, defined by aromatic amino acids and a structured water molecule, rather than the carboxylic acid and amide side chains and a structured water molecule, rather than the carboxylic acid and amide side chains that are features of transport and other carbohydrate binding proteins. A trisaccharide epitope of a branched bacterial lipopolysaccharide fills this hydrophobic pocket (8 A deep by 7 A wide) in an entropy-assisted association (association constant = 2.05 x 10(5) liters per mole, enthalpy = -20.5 +/- 1.7 kilojoules per mole, and temperature times entropy = +10.0 +/- 2.9 kilojoules per mole). The requirement for the complementarity of van der Waals surfaces and the requirements of saccharide-saccharide and protein-saccharide hydrogen-bonding networks determine the antigen conformation adopted in the bound state.

    • Organizational Affiliation: 

    Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)A [auth L]215Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)B [auth H]219Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-2)-[alpha-D-Abequopyranose-(1-3)]alpha-D-mannopyranoseC [auth A]3N/A
Glycosylation Resources
GlyTouCan:  G33761NS
GlyCosmos:  G33761NS
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA		A [auth L]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.3α = 90
b = 128.6β = 90
c = 79.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 1994-01-31 
    • Deposition Author(s): Cygler, M.

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary