6ARC

Monoclinic EutL - structure determined from merged "Group 1" data

6ARC の概要

• エントリーDOI: 10.2210/pdb6arc/pdb
• 分子名称: Ethanolamine utilization protein, SODIUM ION, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: bacterial microcompartment, shell protein, tandem bmc-domain, transport protein
• 由来する生物種: Clostridium perfringens
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 71208.55

構造登録者

Thompson, M.C.,Cascio, D.,Yeates, T.O. (登録日: 2017-08-22, 公開日: 2017-10-11, 最終更新日: 2024-03-13)

主引用文献

Thompson, M.C.,Cascio, D.,Yeates, T.O.
Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism.
Acta Crystallogr D Struct Biol, 74:411-421, 2018

PubMed Abstract: Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

PubMed: 29717712
DOI: 10.1107/S2059798318003479

実験手法

X-RAY DIFFRACTION (1.9 Å)