1OUZ

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Integration Host Factor Alpha-subunitD [auth A]99Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12))
Explore P0A6X7 
Go to UniProtKB:  P0A6X7
Entity Groups  
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UniProt GroupP0A6X7
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Integration Host Factor Beta-subunitE [auth B]94Escherichia coliMutation(s): 1 
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
Explore P0A6Y1 
Go to UniProtKB:  P0A6Y1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6Y1
Sequence Annotations
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Entity ID: 1
MoleculeChains LengthOrganismImage
Phage lambda H' siteA [auth C]35N/A
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'B [auth D]15N/A
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
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]20N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding 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 = 46.799α = 90
b = 60.107β = 90
c = 181.179γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description