3CHB

CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1006/jmbi.1998.2076

  • 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 ...

    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.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biological Structure, Biomolecular Structure Center, University of Washington, Seattle, WA, 98195-7742, USA. merritt@u.washington.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLERA TOXIN
D, E, F, G, H
104Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: ctxB (toxB)
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  P01556
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
E, G, H
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
D, E, F, G, H
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
D, E, F, G, H
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
D, F
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NGA
Query on NGA

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Download CCD File 
D, E, F, G, H
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
G
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
D, E, F, G, H
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.124α = 90.00
b = 66.176β = 106.33
c = 78.221γ = 90.00
Software Package:
Software NamePurpose
SHELX-96refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance