7Z7W

REP-related Chom18 variant with double GC base pairing

7Z7W の概要

• エントリーDOI: 10.2210/pdb7z7w/pdb
• 分子名称: Chom18-GC DNA, STRONTIUM ION (2 entities in total)
• 機能のキーワード: mismatch, non-canonical, base pair, double helix, dna
• 由来する生物種: Cardiobacterium hominis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 5607.16

構造登録者

Svoboda, J.,Schneider, B.,Berdar, D.,Kolenko, P. (登録日: 2022-03-16, 公開日: 2023-03-29, 最終更新日: 2024-02-07)

主引用文献

Svoboda, J.,Berdar, D.,Kolenko, P.,Cerny, J.,Novakova, Z.,Pavlicek, J.,Schneider, B.
Conformation-based refinement of 18-mer DNA structures.
Acta Crystallogr D Struct Biol, 79:655-665, 2023

PubMed Abstract: Nine new crystal structures of CG-rich DNA 18-mers with the sequence 5'-GGTGGGGGC-XZ-GCCCCACC-3', which are related to the bacterial repetitive extragenic palindromes, are reported. 18-mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18-mers crystallized as A-form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC-driven protocol significantly helped to stabilize the structure refinement. The NtC-driven refinement protocol can be adapted to other low-resolution data such as cryo-EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed.

PubMed: 37338420
DOI: 10.1107/S2059798323004679

実験手法

X-RAY DIFFRACTION (2.75 Å)