8D7A

Crystal structure of hen egg white lysozyme at 200 Kelvin (Triplicate)

8D7A の概要

• エントリーDOI: 10.2210/pdb8d7a/pdb
• 分子名称: Lysozyme C, SODIUM ION, CHLORIDE ION, ... (5 entities in total)
• 機能のキーワード: antimicrobial, bacteriolytic enzyme, glycosidase, hydrolase
• 由来する生物種: Gallus gallus (chicken)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 14786.51

構造登録者

Ribeiro, F.S.,Lima, L.M.T.R. (登録日: 2022-06-07, 公開日: 2023-05-10, 最終更新日: 2024-10-23)

主引用文献

de Sa Ribeiro, F.,Lima, L.M.T.R.
Linking B-factor and temperature-induced conformational transition.
Biophys.Chem., 298:107027-107027, 2023

PubMed Abstract: The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducible validation against conformational changes against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with conformational changes of the protein. We obtained the crystal protein structure coordinates and B-factors at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K). The exponential thermal dependence of B-factor as a function of temperature was equal for both the diffraction intensity data (Wilson B-factor) and for all modeled atoms of the system (protein and non-protein atoms), with a thermal diffusion constant of about 0.0045 K, similar for all atoms. The extrapolated B-factor at zero Kelvin (or zero-point fluctuation) varies among the atoms, although with no apparent correlation with temperature-dependent protein conformational changes. These data suggest that the thermal vibration of the atom does not necessarily correlate with the conformational dynamics of the protein.

PubMed: 37172417
DOI: 10.1016/j.bpc.2023.107027

実験手法

X-RAY DIFFRACTION (1.5 Å)