8D5W

Crystal structure of hen egg white lysozyme at 125 Kelvin

Summary for 8D5W

• Entry DOI: 10.2210/pdb8d5w/pdb
• Descriptor: Lysozyme C, SODIUM ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: antimicrobial, bacteriolytic enzyme, glycosidase, hydrolase
• Biological source: Gallus gallus (chicken)
• Total number of polymer chains: 1
• Total formula weight: 14786.51

Authors

Ribeiro, F.S.,Lima, L.M.T.R. (deposition date: 2022-06-06, release date: 2023-05-10, Last modification date: 2024-10-16)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.499 Å)