2GA4

Stx2 with adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding of adenine to Stx2, the protein toxin from Escherichia coli O157:H7.

Fraser, M.E.Cherney, M.M.Marcato, P.Mulvey, G.L.Armstrong, G.D.James, M.N.

(2006) Acta Crystallogr.,Sect.F 62: 627-630

  • DOI: 10.1107/S1744309106021968

  • PubMed Abstract: 
  • Stx2 is a protein toxin whose catalytic subunit acts as an N-glycosidase to depurinate a specific adenine base from 28S rRNA. In the holotoxin, the catalytic portion, A1, is linked to the rest of the A subunit, A2, and A2 interacts with the pentameri ...

    Stx2 is a protein toxin whose catalytic subunit acts as an N-glycosidase to depurinate a specific adenine base from 28S rRNA. In the holotoxin, the catalytic portion, A1, is linked to the rest of the A subunit, A2, and A2 interacts with the pentameric ring formed by the five B subunits. In order to test whether the holotoxin is active as an N-glycosidase, Stx2 was crystallized in the presence of adenosine and adenine. The crystals diffracted to approximately 1.8 angstroms and showed clear electron density for adenine in the active site. Adenosine had been cleaved, proving that Stx2 is an active N-glycosidase. While the holotoxin is active against small substrates, it would be expected that the B subunits would interfere with the binding of the 28S rRNA.


    Organizational Affiliation

    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary AB T2N 1N4, Canada. frasm@ucalgary.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shiga-like toxin II subunit A
A
297Enterobacteria phage 933WGene Names: stxA2 (stx2A)
EC: 3.2.2.22
Find proteins for P09385 (Enterobacteria phage 933W)
Go to UniProtKB:  P09385
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Shiga-like toxin II subunit B
B, C, D, E, F
70Enterobacteria phage 933WGene Names: stxB2 (stx2B)
Find proteins for P09386 (Enterobacteria phage 933W)
Go to UniProtKB:  P09386
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PS
Query on 1PS

Download SDF File 
Download CCD File 
B, C, D, F
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
1-(3-SULFOPROPYL) PYRIDINIUM, PPS
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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Download CCD File 
A, C, D, E
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ADE
Query on ADE

Download SDF File 
Download CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.156 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 144.550α = 90.00
b = 144.550β = 90.00
c = 59.420γ = 120.00
Software Package:
Software NamePurpose
XFITdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-03-07 
  • Released Date: 2006-07-11 
  • Deposition Author(s): Fraser, M.E.

Revision History 

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description