4OCB

Z-DNA dodecamer d(CGCGCGCGCGCG)2 at 0.75 A resolution solved by P-SAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.75 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution

Luo, Z.Dauter, M.Dauter, Z.

(2014) Acta Crystallogr D Biol Crystallogr D70: 1790-1800

  • DOI: 10.1107/S1399004714004684
  • Primary Citation of Related Structures:  
    4OCB

  • PubMed Abstract: 
  • A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was ...

    A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12.2% and an R(free) of 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: Z(I), with the phosphate groups inclined towards the inside of the helix, and Z(II), with the phosphate groups rotated towards the outside of the helix.


    Organizational Affiliation

    Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    d(CGCGCGCGCGCG)2 duplexA12N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 0.75 Å
    • R-Value Free: 0.134 
    • R-Value Work: 0.122 
    • R-Value Observed: 0.122 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 48.484α = 90
    b = 19.546β = 116.36
    c = 31.224γ = 90
    Software Package:
    Software NamePurpose
    NE-CATdata collection
    SHELXDphasing
    SHELXL-97refinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-01-22
      Type: Initial release
    • Version 1.1: 2014-07-16
      Changes: Database references