4OCB

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

PDB DOI: https://doi.org/10.2210/pdb4OCB/pdb
NAKB: 4OCB

Classification: DNA
Mutation(s): No

Deposited: 2014-01-08 Released: 2014-01-22
Deposition Author(s): Luo, Z., Dauter, M., Dauter, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.75 Å
R-Value Free:
0.134 (Depositor), 0.140 (DCC)
R-Value Work:
0.122 (Depositor), 0.130 (DCC)
R-Value Observed:
0.122 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 25004957 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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 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.