1D13

MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)

1D13 の概要

• エントリーDOI: 10.2210/pdb1d13/pdb
• 分子名称: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3') (2 entities in total)
• 機能のキーワード: a-dna, double helix, dna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 3045.99

構造登録者

Frederick, C.A.,Quigley, G.J.,Teng, M.-K.,Coll, M.,Van Der Marel, G.A.,Van Boom, J.H.,Rich, A.,Wang, A.H.-J. (登録日: 1989-10-20, 公開日: 1990-10-15, 最終更新日: 2024-02-07)

主引用文献

Frederick, C.A.,Quigley, G.J.,Teng, M.K.,Coll, M.,Van der Marel, G.A.,Van Boom, J.H.,Rich, A.,Wang, A.H.
Molecular structure of an A-DNA decamer d(ACCGGCCGGT).
Eur.J.Biochem., 181:295-307, 1989

PubMed Abstract: The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6(1)22. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8-12 degrees) resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 degrees, and a base-pair-tilt angle of 18.2 degrees. However, the CpG step in this molecule has a low local-twist angle of 24.5 degrees, similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.

PubMed: 2714286
DOI: 10.1111/j.1432-1033.1989.tb14724.x

実験手法

X-RAY DIFFRACTION (2 Å)