3LZT

REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION

Summary for 3LZT

• Entry DOI: 10.2210/pdb3lzt/pdb
• Descriptor: LYSOZYME, NITRATE ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: hydrolase, o-glycosyl, glycosidase
• Biological source: Gallus gallus (chicken)
• Cellular location: Secreted: P00698
• Total number of polymer chains: 1
• Total formula weight: 14880.32

Authors

Walsh, M.A.,Schneider, T.,Sieker, L.C.,Dauter, Z.,Lamzin, V.,Wilson, K.S. (deposition date: 1997-03-23, release date: 1998-03-25, Last modification date: 2024-10-09)

Primary citation

Walsh, M.A.,Schneider, T.R.,Sieker, L.C.,Dauter, Z.,Lamzin, V.S.,Wilson, K.S.
Refinement of triclinic hen egg-white lysozyme at atomic resolution.
Acta Crystallogr.,Sect.D, 54:522-546, 1998

PubMed Abstract: X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.

PubMed: 9761848
DOI: 10.1107/S0907444997013656

Experimental method

X-RAY DIFFRACTION (0.925 Å)