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 

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.,Sect.D D70: 1790-1800

  • DOI: 10.1107/S1399004714004684
  • Also Cited By: 4R15

  • 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.484α = 90.00
b = 19.546β = 116.36
c = 31.224γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
NE-CATdata collection
SHELXDphasing
HKL-2000data reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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