3U89

Crystal structure of one turn of g/c rich b-dna revisited

「3GGB」から置き換えられました

3U89 の概要

• エントリーDOI: 10.2210/pdb3u89/pdb
• 関連するPDBエントリー: 3GGI 3GGK
• 分子名称: 5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3', MAGNESIUM ION (3 entities in total)
• 機能のキーワード: b-dna, dna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 3167.52

構造登録者

Maehigashi, T.,Woods, K.K.,Moulaei, T.,Komeda, S.,Williams, L.D. (登録日: 2011-10-16, 公開日: 2011-11-09, 最終更新日: 2023-09-13)

主引用文献

Maehigashi, T.,Hsiao, C.,Woods, K.K.,Moulaei, T.,Hud, N.V.,Williams, L.D.
B-DNA structure is intrinsically polymorphic: even at the level of base pair positions.
Nucleic Acids Res., 40:3714-3722, 2012

PubMed Abstract: Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.

PubMed: 22180536
DOI: 10.1093/nar/gkr1168

実験手法

X-RAY DIFFRACTION (0.96 Å)