2IIF

single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending

Bao, Q.Chen, H.Liu, Y.Yan, J.Droge, P.Davey, C.A.

(2007) J.Mol.Biol. 367: 731-740

  • DOI: 10.1016/j.jmb.2006.09.082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Architectural proteins that reconfigure the paths of DNA segments are required for the establishment of functional interfaces in many genomic transactions. A single-chain derivative of the DNA architectural protein integration host factor was found t ...

    Architectural proteins that reconfigure the paths of DNA segments are required for the establishment of functional interfaces in many genomic transactions. A single-chain derivative of the DNA architectural protein integration host factor was found to adopt two stable conformational states in complex with a specific DNA target. In the so-called open state, the degree of protein-induced DNA bending is reduced significantly compared with the closed state. The conformational switch between these states is controlled by divalent metal binding in two electronegative zones arising from the lysine-to-glutamate substitution in the protein body proximal to the phosphate backbone of one DNA arm. We show that this switch can be employed to control the efficiency of site-specific recombination catalyzed by lambda integrase. Introduction of acidic residues at the protein-DNA interface holds potential for the design of metal-mediated switches for the investigation of functional relationships.


    Related Citations: 
    • Activation of site-specific DNA integration in human cells by a single chain integration host factor
      Corona, T.,Bao, Q.,Christ, N.,Schwartz, T.,Li, J.,Droege, P.
      (2003) Nucleic Acids Res. 31: 5140
    • Single-chain integration host factors as probes for high-precision nucleoprotein complex formation
      Bao, Q.,Christ, N.,Droege, P.
      (2004) Gene 343: 99


    Organizational Affiliation

    Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Integration host factor
A
204Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ihfA (hid, himA), ihfB (himD, hip)
Find proteins for P0A6X7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6X7
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Y1
Entity ID: 1
MoleculeChainsLengthOrganism
Phage P H' siteC35synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3')D15synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3')E20synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, D, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.239α = 90.00
b = 54.444β = 90.00
c = 177.865γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    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: 2017-08-09
    Type: Source and taxonomy
  • Version 1.4: 2017-08-16
    Type: Source and taxonomy