5YRX

Crystal structure of a hypothetical protein Rv3716c from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


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Literature

Structural and biophysical characterization of Rv3716c, a hypothetical protein from Mycobacterium tuberculosis

Gopalan, A.Deka, G.Prabhavathi, M.Savithri, H.S.Murthy, M.R.N.Raja, A.

(2018) Biochem. Biophys. Res. Commun. 495: 982-987

  • DOI: 10.1016/j.bbrc.2017.11.093

  • PubMed Abstract: 
  • Latent tuberculosis (TB) is the main hurdle in reaching the goal of "Stop TB 2050". Tuberculin skin and Interferon-gamma release assay tests used currently for the diagnosis of TB infection cannot distinguish between active disease and latent tubercu ...

    Latent tuberculosis (TB) is the main hurdle in reaching the goal of "Stop TB 2050". Tuberculin skin and Interferon-gamma release assay tests used currently for the diagnosis of TB infection cannot distinguish between active disease and latent tuberculosis infection (LTBI) and hence new and sensitive protein markers need to be identified for the diagnosis. A protein Rv3716c from Mycobacterium tuberculosis (MtbRv3716c) has been identified as a potential surrogate marker for the diagnosis of LTBI. Here, we present characterization of MtbRv3716c (∼13 kDa) using both biophysical and X-Ray crystallographic methods. EMSA study showed that MtbRv3716c binds to double stranded DNA. X-ray diffraction data collected on a crystal of MtbRv3716c at 1.9 Å resolution was used for structure determination using the molecular replacement method. Significant electron density was not observed for the N-terminal 21 and C-terminal 41 residues in the final electron density map. The C- terminal disordered region is proline rich and displays characteristics of intrinsically disordered proteins. Although the crystal asymmetric unit contained a protomer, a tight dimer could be generated by the application of the crystal two-fold symmetry parallel to the b axis. Packing of dimers in the crystal is mediated by a cadmium ion (Cd 2+ ) occurring at the interface of two dimers. Molecular packing analysis reveals large cavities that are probably occupied by the disordered segments of the N- and C-termini. Structural comparison with other homologous hypothetical DNA binding proteins (PDB codes: 1PUG, 1YBX) highlights structural features that might be significant for DNA binding.


    Organizational Affiliation

    National Institute for Research in Tuberculosis, Chennai 600031, India.,Biochemistry Department, Indian Institute of Science, Bangalore 560012, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: mrn@iisc.ac.in.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoid-associated protein Rv3716c
A
139Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Find proteins for P9WNR9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNR9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 35.110α = 90.00
b = 183.750β = 90.00
c = 37.250γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Science and TechnologyIndiaSR/S2/JCB-12/2005/9.5.2006

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release