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

Experimental Data Snapshot

  • Resolution: 3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history


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: --


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shiga-like toxin 2 subunit B
A, B, C, D, E
72Enterobacteria phage 933WMutation(s): 0 
Gene Names: stxB2 (stx2B)
Find proteins for P09386 (Enterobacteria phage 933W)
Go to UniProtKB:  P09386
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
F, G, H, I, J
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Resolution: 3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 186.490α = 90.00
b = 186.490β = 90.00
c = 75.500γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

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

Revision History 

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