4PWS

Crystal structure of secreted proline rich antigen MTC28 (Rv0040c) at 2.15 A with bound chloride from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure-based Epitope Mapping of Mycobacterium tuberculosis Secretary Antigen MTC28

Kundu, P.Biswas, R.Mukherjee, S.Reinhard, L.Dutta, A.Mueller-Dieckmann, J.Weiss, M.S.Pal, N.K.Das, A.K.

(2016) J Biol Chem 291: 13943-13954

  • DOI: https://doi.org/10.1074/jbc.M116.726422
  • Primary Citation of Related Structures:  
    4OL4, 4PWS

  • PubMed Abstract: 

    Secretary proteins of Mycobacterium tuberculosis are key players of the mycobacterial infection pathway. MTC28 is a 28-kDa proline-rich secretary antigen of Mycobacterium tuberculosis and is only conserved in pathogenic strains of mycobacteria. Here we report the crystal structure of MTC28 at 2.8- and 2.15-Å resolutions for the structure-based epitope design. MTC28 shares a "mog1p"-fold consisting of seven antiparallel β strands stacked between α helices. Five probable epitopes have been located on a solvent-accessible flexible region by computational analysis of the structure of MTC28. Simultaneously, the protein is digested with trypsin and the resulting fragments are purified by HPLC. Such 10 purified peptide fragments are screened against sera from patients infected with pulmonary tuberculosis (PTB). Two of these 10 fragments, namely (127)ALDITLPMPPR(137) and (138)WTQVPDPNVPDAFVVIADR(156),are found to be major immunogenic epitopes that are localized on the outer surface of the protein molecule and are part of a single continuous epitope that have been predicted in silico Mutagenesis and antibody inhibition studies are in accordance with the results obtained from epitope mapping.


  • Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline-rich 28 kDa antigen289Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT0046mtc28MTCY21D4.03cRv0040c
UniProt
Find proteins for P9WIM9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIM9 
Go to UniProtKB:  P9WIM9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIM9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.41α = 90
b = 101.41β = 90
c = 67.69γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Data collection
  • Version 1.2: 2017-01-11
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Data collection, Database references
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description