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 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.jmb.2012.01.019

  • 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-aff ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Colicin-E2 immunity protein
A
94Escherichia coliMutation(s): 0 
Gene Names: imm (ceiB)
Find proteins for P04482 (Escherichia coli)
Go to UniProtKB:  P04482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin-E2
B
134Escherichia coliMutation(s): 0 
Gene Names: col (ceaB)
EC: 3.1.-.-
Find proteins for P04419 (Escherichia coli)
Go to UniProtKB:  P04419
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.814α = 90.00
b = 53.277β = 90.00
c = 32.785γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
SCALAdata scaling
MOLREPphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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