1OWG

Crystal structure of WT IHF complexed with an altered H' site (T44A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Integration Host Factor Alpha-subunitD [auth A]99Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6X7
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Integration Host Factor beta-subunitE [auth B]94Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6Y1
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Phage lambda H' siteA [auth C]35N/A
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3'B [auth D]15N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      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
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Binding Affinity Annotations 
      IDSourceBinding Affinity
      DNA PDBBind:  1OWG Kd: 200 (nM) from 1 assay(s)
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.10 Å
      • R-Value Free: 0.261 
      • R-Value Work: 0.226 
      • R-Value Observed: 0.226 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 46.66α = 90
      b = 58.832β = 90
      c = 181.314γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report




      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