The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site.Merritt, E.A., Kuhn, P., Sarfaty, S., Erbe, J.L., Holmes, R.K., Hol, W.G.
(1998) J.Mol.Biol. 282: 1043-1059
- PubMed: 9753553
- DOI: 10.1006/jmbi.1998.2076
- PubMed Abstract:
- Crystal Structure of Cholera Toxin B-Pentamer Bound to Receptor Gm1 Pentasaccharide
Merritt, E.A.,Sarfaty, S.,Van Den Akker, F.,L'Hoir, C.,Martial, J.A.,Hol, W.G.
(1994) Protein Sci. 3: 166
- Structural Studies of Receptor Binding by Cholera Toxin Mutants
Merritt, E.A.,Sarfaty, S.,Jobling, M.G.,Chang, T.,Holmes, R.K.,Hirst, T.R.,Hol, W.G.
(1997) Protein Sci. 6: 1516
Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the ganglioside GM1 receptor pentasaccharide diffract to near-atomic resolution. We have refined the crystallographic model for this complex using anisotropic displacement parameters ...
Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the ganglioside GM1 receptor pentasaccharide diffract to near-atomic resolution. We have refined the crystallographic model for this complex using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.129 for all observed Bragg reflections in the resolution range 22 A to 1.25 A. Remarkably few residues show evidence of discrete conformational disorder. A notable exception is a minority conformation found for the Cys9 side-chain, which implies that the Cys9-Cys86 disulfide linkage is incompletely formed. In all five crystallographically independent instances, the peptide backbone in the region of the receptor-binding site shows evidence of strain, including unusual bond lengths and angles, and a highly non-planar (omega=153.7(7) degrees) peptide group between residues Gln49 and Val50. The location of well-ordered water molecules at the protein surface is notable reproduced among the five crystallographically independent copies of the peptide chain, both at the receptor-binding site and elsewhere. The 5-fold non-crystallographic symmetry of this complex allows an evaluation of the accuracy, reproducibility, and derived error estimates from refinement of large structures at near-atomic resolution. We find that blocked-matrix treatment of parameter covariance underestimates the uncertainty of atomic positions in the final model by approximately 10% relative to estimates based either on full-matrix inversion or on the 5-fold non-crystallographic symmetry.
Department of Biological Structure, Biomolecular Structure Center, University of Washington, Seattle, WA, 98195-7742, USA. email@example.com