3QBA

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray)

3QBA の概要

• エントリーDOI: 10.2210/pdb3qba/pdb
• 関連するPDBエントリー: 1ICK 1V9G 1WOE 3QBB
• 分子名称: Z-DNA (2 entities in total)
• 機能のキーワード: z-dna, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3460.45

構造登録者

Fenn, T.D.,Schnieders, M.J.,Mustyakimov, M.,Wu, C.,Langan, P.,Pande, V.S.,Brunger, A.T. (登録日: 2011-01-12, 公開日: 2011-03-02, 最終更新日: 2024-02-21)

主引用文献

Fenn, T.D.,Schnieders, M.J.,Mustyakimov, M.,Wu, C.,Langan, P.,Pande, V.S.,Brunger, A.T.
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
Structure, 19:523-533, 2011

PubMed Abstract: Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.

PubMed: 21481775
DOI: 10.1016/j.str.2011.01.015

実験手法

NEUTRON DIFFRACTION (1.4 Å)
X-RAY DIFFRACTION (1.53 Å)