| Autor: |
Merritt, Ethan A., Kuhn, Peter, Sarfaty, Steve, Erbe, Jarrod L., Holmes, Randall K., Hol, Wim G.J. |
| Zdroj: |
JMB Online (Journal of Molecular Biology); October 09, 1998, Vol. 282 Issue: 5 p1043-1059, 17p |
| Abstrakt: |
Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the ganglioside GM1receptor 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 (ω=153.7(7)°) 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. |
| Databáze: |
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