6SVW

Reference structure of bovine trypsin (even frames of crystal x33)

6SVW の概要

• エントリーDOI: 10.2210/pdb6svw/pdb
• 分子名称: Cationic trypsin, CALCIUM ION, BENZAMIDINE, ... (5 entities in total)
• 機能のキーワード: bovine trypsin, hydrolase, terahertz irradiation, even frames, x33
• 由来する生物種: Bos taurus (cattle)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23676.64

構造登録者

Ahlberg Gagner, V.,Lundholm, I.,Garcia-Bonete, M.J.,Rodilla, H.,Friedman, R.,Zhaunerchyk, V.,Bourenkov, G.,Schneider, T.,Stake, J.,Katona, G. (登録日: 2019-09-19, 公開日: 2020-01-22, 最終更新日: 2024-10-23)

主引用文献

Gagner, V.A.,Lundholm, I.,Garcia-Bonete, M.J.,Rodilla, H.,Friedman, R.,Zhaunerchyk, V.,Bourenkov, G.,Schneider, T.,Stake, J.,Katona, G.
Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.
Sci Rep, 9:19281-19281, 2019

PubMed Abstract: Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

PubMed: 31848402
DOI: 10.1038/s41598-019-55777-5

実験手法

X-RAY DIFFRACTION (1.16 Å)