Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.48 kDa 
• Atom Count: 3,101 
• Modelled Residue Count: 260 
• Deposited Residue Count: 263 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

 1OUZ

Crystal structure of a mutant IHF (BetaE44A) complexed with a variant H' Site (T44A)

• PDB DOI: 10.2210/pdb1OUZ/pdb
• NDB: PD0405

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-03-25 Released: 2003-07-15 
• Deposition Author(s): Lynch, T.W., Read, E.K., Mattis, A.N., Gardner, J.F., Rice, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.271 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 

Literature

Integration Host Factor: putting a twist on protein-DNA recognition

Lynch, T.W., Read, E.K., Mattis, A.N., Gardner, J.F., Rice, P.A.

(2003) J Mol Biol 330: 493-502

• PubMed: 12842466 
• DOI: 10.1016/s0022-2836(03)00529-1
• Primary Citation of Related Structures:  
  1OUZ, 1OWF, 1OWG


• PubMed Abstract: 
  

Integration host factor (IHF) is a DNA-bending protein that recognizes its cognate sites through indirect readout. Previous studies have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center position of a conserved TTR motif in its binding site, and that substitution of betaGlu44 with Ala prevented IHF from discriminating between A and T at this position. We have determined the crystal structures and relative binding affinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs. Comparison of these structures reveals that DNA twist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on the dinucleotide step and not on the bound IHF variant.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The University of Chicago, 920 E 58th Street CLSC 221, Chicago, IL 60637, USA.

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Integration Host Factor Alpha-subunit	D [auth A]	99	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12)) Explore P0A6X7  Go to UniProtKB:  P0A6X7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Integration Host Factor Beta-subunit	E [auth B]	94	Escherichia coli	Mutation(s): 1
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12)) Explore P0A6Y1  Go to UniProtKB:  P0A6Y1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Phage lambda H' site	A [auth C]	35	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'	B [auth D]	15	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*AP*GP*CP*AP*CP*C)-3'	C [auth E]	20	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1OUZ	Kd: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.271 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.799	α = 90
b = 60.107	β = 90
c = 181.179	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-15 
Deposition Author(s): Lynch, T.W., Read, E.K., Mattis, A.N., Gardner, J.F., Rice, P.A.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references