3CHB

CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE

Summary for 3CHB

• Entry DOI: 10.2210/pdb3chb/pdb
• Descriptor: CHOLERA TOXIN, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: toxin, toxin-receptor complex, pentasaccharide
• Biological source: Vibrio cholerae
• Cellular location: Secreted: P01556
• Total number of polymer chains: 5
• Total formula weight: 64288.48

Authors

Merritt, E.A.,Hol, W.G.J. (deposition date: 1998-03-24, release date: 1998-08-12, Last modification date: 2023-08-09)

Primary citation

Merritt, E.A.,Kuhn, P.,Sarfaty, S.,Erbe, J.L.,Holmes, R.K.,Hol, W.G.
The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site.
J.Mol.Biol., 282:1043-1059, 1998

PubMed Abstract: 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.

PubMed: 9753553
DOI: 10.1006/jmbi.1998.2076

Experimental method

X-RAY DIFFRACTION (1.25 Å)