Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.76 kDa 
• Atom Count: 3,318 
• Modelled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

 2IIE

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

• PDB DOI: 10.2210/pdb2IIE/pdb
• NDB: PD0878

• Classification: RECOMBINATION/DNA
• Organism(s): synthetic construct, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-28 Released: 2007-02-20 
• Deposition Author(s): Bao, Q., Droege, P., Davey, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.272 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

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

• PubMed: 17276457 
• DOI: 10.1016/j.jmb.2006.09.082
• Primary Citation of Related Structures:  
  2IIE, 2IIF


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Integration host factor	D [auth A]	204	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12)) Explore P0A6X7  Go to UniProtKB:  P0A6X7
Find proteins for P0A6Y1 (Escherichia coli (strain K12)) Explore P0A6Y1  Go to UniProtKB:  P0A6Y1
UniProt Groups	P0A6Y1P0A6X7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Phage P H' site	A [auth C]	35	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3')	B [auth D]	15	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3')	C [auth E]	20	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth C], F [auth D], G [auth D], H [auth E], I [auth A], J [auth A], K [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.272 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.371	α = 90
b = 55.311	β = 90
c = 177.833	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Bao, Q., Droege, P., Davey, C.A.

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-09
  Changes: Source and taxonomy
• Version 1.4: 2017-08-16
  Changes: Source and taxonomy