1CW9

DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

A structural snapshot of base-pair opening in DNA.

van Aalten, D.M., Erlanson, D.A., Verdine, G.L., Joshua-Tor, L.

(1999) Proc Natl Acad Sci U S A 96: 11809-11814

  • DOI: 10.1073/pnas.96.21.11809
  • Primary Citation of Related Structures:  
    1CW9

  • PubMed Abstract: 

    • The response of double-helical DNA to torsional stress may be a driving force for many processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the ...

    The response of double-helical DNA to torsional stress may be a driving force for many processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine bases depicts how the duplex can accommodate such torsional stress. We have captured in the same crystal two rather different conformational states. One duplex contains a strained crosslink that is stabilized by calcium ion binding in the major groove, directly opposite the crosslink. For the other duplex, the strain in the crosslink is relieved through partial rupture of a base pair and partial extrusion of a cytosine accompanied by helix bending. The sequence used is the target sequence for the HaeIII methylase, and this partially flipped cytosine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics simulations of these structures show an increased mobility for the partially flipped-out cytosine.

    Organizational Affiliation: 

    W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'A, B, C, D10N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CA
    Query on CA
    Download Ideal Coordinates CCD File 
    A
    		CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.55 Å
    • R-Value Free: 0.232 
    • R-Value Work: 0.203 
    • R-Value Observed: 0.203 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 34.435α = 90
    b = 43.18β = 90
    c = 72.412γ = 90
    Software Package:
    Software NamePurpose
    AMoREphasing
    CNSrefinement
    MAR345data collection
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1999-10-14
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-02-01
      Changes: Structure summary
    • Version 1.4: 2017-10-04
      Changes: Refinement description