3UID | pdb_00003uid

Crystal Structure of Protein Ms6760 from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.213 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response.

Bajaj, R.A.Arbing, M.A.Shin, A.Cascio, D.Miallau, L.

(2016) Acta Crystallogr F Struct Biol Commun 72: 863-869

  • DOI: https://doi.org/10.1107/S2053230X16017957
  • Primary Citation Related Structures: 
    3UID

  • PubMed Abstract: 

    The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin-antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate-latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novel TA system involved in Mycobacterium tuberculosis latency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.


  • Organizational Affiliation
    • UCLA-DOE Institute and Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA.

Macromolecule Content 

  • Total Structure Weight: 37.13 kDa 
  • Atom Count: 2,733 
  • Modeled Residue Count: 320 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
A, B
168Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_6760
UniProt
Find proteins for A0R731 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R731 
Go to UniProtKB:  A0R731
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R731
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.213 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.32α = 90
b = 60.21β = 90
c = 100.98γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description