1IJW

Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Testing water-mediated DNA recognition by the Hin recombinase.

Chiu, T.K.Sohn, C.Dickerson, R.E.Johnson, R.C.

(2002) EMBO J 21: 801-814

  • DOI: 10.1093/emboj/21.4.801
  • Primary Citation of Related Structures:  
    1IJW, 1JJ8, 1JJ6, 1JKQ, 1JKP, 1JKO, 1JKR

  • PubMed Abstract: 
  • The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were ...

    The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were solved as part of the present study, have revealed that two ordered water molecules are present within the major groove interface. In this report, we test the importance of these waters directly by X-ray crystal structure analysis of complexes with four mutant DNA sequences. These structures, combined with their Hin-binding properties, provide strong support for the critical importance of one of the intermediate waters. A lesser but demonstrable role is ascribed to the second water molecule. The mutant structures also illustrate the prominent roles of thymine methyls both in stabilizing intermediate waters and in interfering with water or amino acid side chain interactions with DNA.


    Related Citations: 
    • How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase.
      Chiu, T.K.
      (2001) Thesis --: 145
    • Hin Recombinase Bound to DNA: the Origin of Specificity in Major and Minor Groove Interactions.
      Feng, J.A., Johnson, R.C., Dickerson, R.E.
      (1994) Science 263: 348

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-INVERTASE HINC52N/AMutation(s): 0 
Find proteins for P03013 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P03013 
Go to UniProtKB:  P03013
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'A14N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*TP*(CBR)P*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'B14N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      TRS
      Query on TRS

      Download CCD File 
      B, C
      2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
      C4 H12 N O3
      LENZDBCJOHFCAS-UHFFFAOYSA-O
       Ligand Interaction
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      DNAKd :  3.799999952316284   nM  PDBBind
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.278 
      • R-Value Work: 0.223 
      • R-Value Observed: 0.223 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 85.749α = 90
      b = 81.136β = 90
      c = 44.596γ = 90
      Software Package:
      Software NamePurpose
      SOLVEphasing
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2002-02-22
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance