4OCB

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

4OCB の概要

• エントリーDOI: 10.2210/pdb4ocb/pdb
• 関連するPDBエントリー: 3P4J
• 分子名称: d(CGCGCGCGCGCG)2 duplex (2 entities in total)
• 機能のキーワード: z-dna dodecamer duplex, dna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 3665.37

構造登録者

Luo, Z.,Dauter, M.,Dauter, Z. (登録日: 2014-01-08, 公開日: 2014-01-22, 最終更新日: 2024-02-28)

主引用文献

Luo, Z.,Dauter, M.,Dauter, Z.
Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution
Acta Crystallogr.,Sect.D, D70:1790-1800, 2014

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.

PubMed: 25004957
DOI: 10.1107/S1399004714004684

実験手法

X-RAY DIFFRACTION (0.75 Å)