8D8E
Crystal structure of hen egg white lysozyme at 300 Kelvin (Triplicate)
Summary for 8D8E
| Entry DOI | 10.2210/pdb8d8e/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: 2022-06-08, release date: 2023-05-10, Last modification date: 2024-11-20) |
| 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 Cited by 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: 37172417DOI: 10.1016/j.bpc.2023.107027 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.5 Å) |
Structure validation
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