5BUN

Crystal structure of an antigenic outer membrane protein ST50 from Salmonella Typhi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

Guan, H.H.Yoshimura, M.Chuankhayan, P.Lin, C.C.Chen, N.C.Yang, M.C.Ismail, A.Fun, H.K.Chen, C.J.

(2015) Sci Rep 5: 16441-16441

  • DOI: 10.1038/srep16441
  • Primary Citation of Related Structures:  
    5BUN

  • PubMed Abstract: 
  • ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)) ...

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.


    Organizational Affiliation

    Department of Physics, National Tsing Hua University, Hsinchu, 30043, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Outer membrane proteinA, B, C467Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0X1KHE0 (Salmonella typhi)
Explore A0A0X1KHE0 
Go to UniProtKB:  A0A0X1KHE0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG (Subject of Investigation/LOI)
Query on BOG

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth B], G [auth C]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 246.847α = 90
b = 246.847β = 90
c = 65.676γ = 90
Software Package:
Software NamePurpose
XDSdata collection
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary