4WPY

Racemic crystal structure of Rv1738 from Mycobacterium tuberculosis (Form-II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography.

Bunker, R.D.Mandal, K.Bashiri, G.Chaston, J.J.Pentelute, B.L.Lott, J.S.Kent, S.B.Baker, E.N.

(2015) Proc Natl Acad Sci U S A 112: 4310-4315

  • DOI: https://doi.org/10.1073/pnas.1422387112
  • Primary Citation of Related Structures:  
    4WPY, 4WSP

  • PubMed Abstract: 

    Protein 3D structure can be a powerful predictor of function, but it often faces a critical roadblock at the crystallization step. Rv1738, a protein from Mycobacterium tuberculosis that is strongly implicated in the onset of nonreplicating persistence, and thereby latent tuberculosis, resisted extensive attempts at crystallization. Chemical synthesis of the L- and D-enantiomeric forms of Rv1738 enabled facile crystallization of the D/L-racemic mixture. The structure was solved by an ab initio approach that took advantage of the quantized phases characteristic of diffraction by centrosymmetric crystals. The structure, containing L- and D-dimers in a centrosymmetric space group, revealed unexpected homology with bacterial hibernation-promoting factors that bind to ribosomes and suppress translation. This suggests that the functional role of Rv1738 is to contribute to the shutdown of ribosomal protein synthesis during the onset of nonreplicating persistence of M. tuberculosis.


  • Organizational Affiliation

    Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand; and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
protein DL-Rv173894Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for P9WLS2 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WLS2 
Go to UniProtKB:  P9WLS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WLS2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2/c 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.402α = 90
b = 43.989β = 118.44
c = 58.437γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references