3CHB: Cholera Toxin B-Pentamer Complexed With Gm1 Pentasaccharide

Citation:
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.
PDB ID: 3CHBDownload
MMDB ID: 8325
PDB Deposition Date: 1998/3/24
Updated in MMDB: 1998/11
Experimental Method:
x-ray diffraction
Resolution: 1.25  Å
Source Organism:
Similar Structures:
Biological Unit for 3CHB: pentameric; determined by author and by software (PISA)
Molecular Components in 3CHB
Label Count Molecule
Proteins (5 molecules)
5
Cholera Toxin(Gene symbol: VC1456)
Molecule annotation
Chemicals (32 molecules)
1
10
2
5
3
2
4
5
5
5
Molecule information is not avaliable.
6
3
7
2
* Click molecule labels to explore molecular sequence information.

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