7Q3V

Re-refined structure of a type III antifreeze protein isoform HPLC 12

7Q3V の概要

• エントリーDOI: 10.2210/pdb7q3v/pdb
• 分子名称: Type-3 ice-structuring protein HPLC 12 (2 entities in total)
• 機能のキーワード: restrained md refinement scheme, amber, crystal unit cell model, ensemble refinement, antifreeze protein
• 由来する生物種: Zoarces americanus (ocean pout)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 28225.78

構造登録者

Mikhailovskii, O.,Xue, Y.,Jia, Z.,Skrynnikov, N.R. (登録日: 2021-10-28, 公開日: 2022-04-20, 最終更新日: 2024-01-31)

主引用文献

Mikhailovskii, O.,Xue, Y.,Skrynnikov, N.R.
Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber.
Iucrj, 9:114-133, 2022

PubMed Abstract: A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program . The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new -based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower values compared with those reported in the original PDB depositions or obtained by means of the industry-standard program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, -refined structures consistently show superior scores. The new approach offers a highly realistic representation of protein-protein interactions in the crystal, as well as of protein-water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.

PubMed: 35059216
DOI: 10.1107/S2052252521011891

実験手法

X-RAY DIFFRACTION (1.9 Å)