3U43

Crystal structure of the colicin E2 DNase-Im2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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This is version 1.0 of the entry. See complete history


Literature

Structure of the Ultra-High-Affinity Colicin E2 DNase-Im2 Complex.

Wojdyla, J.A.Fleishman, S.J.Baker, D.Kleanthous, C.

(2012) J Mol Biol 417: 79-94

  • DOI: https://doi.org/10.1016/j.jmb.2012.01.019
  • Primary Citation of Related Structures:  
    3U43

  • PubMed Abstract: 

    How proteins achieve high-affinity binding to a specific protein partner while simultaneously excluding all others is a major biological problem that has important implications for protein design. We report the crystal structure of the ultra-high-affinity protein-protein complex between the endonuclease domain of colicin E2 and its cognate immunity (Im) protein, Im2 (K(d)∼10(-)(15) M), which, by comparison to previous structural and biophysical data, provides unprecedented insight into how high affinity and selectivity are achieved in this model family of protein complexes. Our study pinpoints the role of structured water molecules in conjoining hotspot residues that govern stability with residues that control selectivity. A key finding is that a single residue, which in a noncognate context massively destabilizes the complex through frustration, does not participate in specificity directly but rather acts as an organizing center for a multitude of specificity interactions across the interface, many of which are water mediated.


  • Organizational Affiliation

    Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin-E2 immunity protein94Escherichia coliMutation(s): 0 
Gene Names: immceiB
UniProt
Find proteins for P04482 (Escherichia coli)
Explore P04482 
Go to UniProtKB:  P04482
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04482
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin-E2134Escherichia coliMutation(s): 0 
Gene Names: colceaB
EC: 3.1
UniProt
Find proteins for P04419 (Escherichia coli)
Explore P04419 
Go to UniProtKB:  P04419
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04419
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.814α = 90
b = 53.277β = 90
c = 32.785γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release