4WPY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.USA 112: 4310-4315

  • DOI: 10.1073/pnas.1422387112
  • Primary Citation of Related Structures:  

  • 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 persistenc ...

    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

    Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637.,Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637 ted.baker@auckland.ac.nz skent@uchicago.edu.,Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand; and.,Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand; and ted.baker@auckland.ac.nz skent@uchicago.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protein DL-Rv1738
A
94Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Find proteins for P9WLS2 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WLS2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TFA
Query on TFA

Download SDF File 
Download CCD File 
A
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.228 
  • Space Group: C 1 2/c 1
Unit Cell:
Length (Å)Angle (°)
a = 80.402α = 90.00
b = 43.989β = 118.44
c = 58.437γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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