4DTD

Structure and functional characterization of a Vibrio cholerae toxin from the MARTX/VgrG family.

Structural Biology Knowledgebase: 4DTD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DTD

Classification: TOXIN

Total Structure Weight: 44256.86

Macromolecule Entities
Molecule Chains Length Organism Details
VgrG protein A 396 Vibrio cholerae EC#: 6.3.2 IUBMB
Fragment: unp residues 716-1111
Gene Name(s): vgrG1 vgrG-1 VC0395_A1026

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.187
  • Space Group: P 43 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.08 α = 90.00
b = 128.08 β = 90.00
c = 76.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-21
  • Released Date: 2012-08-29
  • Deposition author(s): Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.

Revision History

No revisions since initial release