7KTY

Data clustering and dynamics of chymotrypsinogen average structure

7KTY の概要

• エントリーDOI: 10.2210/pdb7kty/pdb
• 分子名称: Chymotrypsinogen A, SULFATE ION (3 entities in total)
• 機能のキーワード: clustering, dynamics, data analysis, chymotrypsinogen, hydrolase
• 由来する生物種: Bos taurus (Bovine)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25974.23

構造登録者

Nguyen, T.,Phan, K.L.,Kreitler, D.F.,Andrews, L.C.,Gabelli, S.B.,Kozakov, D.,Jakoncic, J.,Shi, W.,Sweet, R.M.,Soares, A.S.,Bernstein, H.J. (登録日: 2020-11-24, 公開日: 2021-03-10, 最終更新日: 2024-11-13)

主引用文献

Nguyen, T.,Phan, K.L.,Kozakov, D.,Gabelli, S.B.,Kreitler, D.F.,Andrews, L.C.,Jakoncic, J.,Sweet, R.M.,Soares, A.S.,Bernstein, H.J.
A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs.
Acta Crystallogr D Struct Biol, 78:268-277, 2022

PubMed Abstract: One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

PubMed: 35234141
DOI: 10.1107/S2059798321013425

実験手法

X-RAY DIFFRACTION (2 Å)