6FE4

Crystal structure of the complex between Shiga toxin Stx2 B subunit and neutralising Nb113


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Specific Neutralization of Stx2a with a Camelid Single Domain Antibody Fragment.

Bernedo-Navarro, R.A.Romao, E.Yano, T.Pinto, J.De Greve, H.Sterckx, Y.G.Muyldermans, S.

(2018) Toxins (Basel) 10

  • DOI: 10.3390/toxins10030108
  • Primary Citation of Related Structures:  
    6FE4

  • PubMed Abstract: 
  • Shiga toxin-producing Escherichia coli (STEC) are a subset of pathogens leading to illnesses such as diarrhea, hemolytic uremic syndrome and even death. The Shiga toxins are the main virulence factors and divided in two groups: Stx1 and Stx2, of which the latter is more frequently associated with severe pathologies in humans ...

    Shiga toxin-producing Escherichia coli (STEC) are a subset of pathogens leading to illnesses such as diarrhea, hemolytic uremic syndrome and even death. The Shiga toxins are the main virulence factors and divided in two groups: Stx1 and Stx2, of which the latter is more frequently associated with severe pathologies in humans.


    Organizational Affiliation

    Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium. serge.muyldermans@vub.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Shiga-like toxin 2 subunit BA, B, C, D, E72Escherichia phage 933WMutation(s): 0 
Gene Names: stxB2stx2BL0104
Find proteins for P09386 (Escherichia phage 933W)
Explore P09386 
Go to UniProtKB:  P09386
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nb113F, G, H, I, J119Vicugna pacosMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.49α = 90
b = 186.49β = 90
c = 75.5γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)BrazilResearch Internship Abroad (BEPE) awarded to Robert Bernedo

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references