5F6M

Isotropic Trypsin Model for Comparison of Diffuse Scattering

5F6M の概要

• エントリーDOI: 10.2210/pdb5f6m/pdb
• 分子名称: Cationic trypsin, CALCIUM ION, BENZAMIDINE, ... (5 entities in total)
• 機能のキーワード: serine protease, hydrolase
• 由来する生物種: Bos taurus (Bovine)
• 細胞内の位置: Secreted, extracellular space: P00760
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23580.58

構造登録者

Van Benschoten, A.H.,Wall, M.E.,Fraser, J.S. (登録日: 2015-12-06, 公開日: 2016-01-06, 最終更新日: 2024-11-13)

主引用文献

Van Benschoten, A.H.,Liu, L.,Gonzalez, A.,Brewster, A.S.,Sauter, N.K.,Fraser, J.S.,Wall, M.E.
Measuring and modeling diffuse scattering in protein X-ray crystallography.
Proc.Natl.Acad.Sci.USA, 113:4069-4074, 2016

PubMed Abstract: X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

PubMed: 27035972
DOI: 10.1073/pnas.1524048113

実験手法

X-RAY DIFFRACTION (1.1 Å)