5VR0

Crystal structure of glucose isomerase from Streptomyces rubiginosus

5VR0 の概要

• エントリーDOI: 10.2210/pdb5vr0/pdb
• 分子名称: Xylose isomerase, (4R)-2-METHYLPENTANE-2,4-DIOL, MANGANESE (II) ION, ... (6 entities in total)
• 機能のキーワード: isomerase(intramolecular oxidoreductase), radiation damage, isomerase, oxidoreductase
• 由来する生物種: Streptomyces rubiginosus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 44057.02

構造登録者

Borek, D.,Otwinowski, Z. (登録日: 2017-05-09, 公開日: 2018-05-02, 最終更新日: 2023-10-04)

主引用文献

Borek, D.,Bromberg, R.,Hattne, J.,Otwinowski, Z.
Real-space analysis of radiation-induced specific changes with independent component analysis.
J Synchrotron Radiat, 25:451-467, 2018

PubMed Abstract: A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identified two components, with the temperature-independent component being responsible for the majority of specific radiation-induced changes at temperatures below 130 K. The patterns of specific temperature-independent radiation-induced changes suggest a contribution from the tunnelling of electron holes as a possible explanation. In the second case, where a group of 22 data sets was collected on a single thaumatin crystal, ICA was used in another type of analysis to separate specific radiation-induced effects happening on different exposure-level scales. Here, ICA identified two components of specific radiation-induced changes that likely result from radiation-induced chemical reactions progressing with different rates at different locations in the structure. In addition, ICA unexpectedly identified the radiation-damage state corresponding to reduced disulfide bridges rather than the zero-dose extrapolated state as the highest contrast structure. The application of ICA to the analysis of specific radiation-induced changes in real space and the data pre-processing for ICA that relies on singular value decomposition, which was used previously in data space to validate a two-component physical model of X-ray radiation-induced changes, are discussed in detail. This work lays a foundation for a better understanding of protein-specific radiation chemistries and provides a framework for analysing effects of specific radiation damage in crystallographic and cryo-EM experiments.

PubMed: 29488925
DOI: 10.1107/S1600577517018148

実験手法

X-RAY DIFFRACTION (1.7 Å)