7YD4 | pdb_00007yd4

Crystal structure of an N terminal truncated secreted protein, Rv0398c from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway.

Saha, R.Mukherjee, S.Singh, B.De, S.Weiss, M.S.Das, A.K.

(2023) Biochem Biophys Res Commun 672: 45-53

  • DOI: https://doi.org/10.1016/j.bbrc.2023.06.029
  • Primary Citation of Related Structures:  
    7YD4

  • PubMed Abstract: 

    Secretory proteins are used by pathogenic bacteria to manipulate the host systems and compete with other microorganisms, thereby enabling their survival in their host. Similar to other bacteria, secretory proteins of Mycobacterium tuberculosis also play a pivotal role in evading immune response within hosts, thereby leading to acute and latent tuberculosis infection. Prokaryotes have several classes of bacterial secretory systems out of which the Sec and Tat pathways are the most conserved in Mtb to transport proteins across the cytoplasmic membrane. Here, we report the crystal structure of a secretory protein, Rv0398c determined to 1.9 Å resolution. The protein comprises a core of antiparallel β sheets surrounded by α helices adopting a unique β sandwich fold. Structural comparison with other secretory proteins in Mtb and other pathogenic bacteria reveals that Rv0398c may be secreted via the Sec pathway. Our structural and in silico analyses thus provide mechanistic insights into the pathway adopted by Mtb to transport out secretory protein, Rv0398c which will facilitate the invasion to the host immune system.


  • Organizational Affiliation
    • Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Possible secreted protein185Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0398c
UniProt
Find proteins for P95206 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P95206 
Go to UniProtKB:  P95206
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95206
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.881α = 90
b = 73.463β = 90
c = 103.724γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)India--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary