3B18

Rv0098 of Mycobacterium tuberculosis with ordered loop between beta-4 and beta-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into the substrate specificity of a thioesterase Rv0098 of mycobacterium tuberculosis through X-ray crystallographic and molecular dynamics studies.

Maity, K.Bajaj, P.Surolia, N.Surolia, A.Suguna, K.

(2012) J Biomol Struct Dyn 29: 973-983

  • DOI: 10.1080/07391102.2012.10507417
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of su ...

    The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of substrate specificities of varying chain length. Molecular dynamics studies demonstrated that certain residues of the substrate binding tunnel are flexible and thus modulate the length of the tunnel. The flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. A combination of crystallographic and molecular dynamics studies thus explained the structural basis of accommodating long chain substrates by Rv0098 of M. tuberculosis.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560 012, India.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein Rv0098/MT0107A183Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv0098
EC: 3.1.2 (UniProt), 3.1.2.2 (UniProt)
Find proteins for P9WM67 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WM67 
Go to UniProtKB:  P9WM67
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAO
Query on DAO

Download CCD File 
A
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.19α = 90
b = 100.19β = 90
c = 100.19γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-06-26 
  • Released Date: 2012-06-06 
  • Deposition Author(s): Maity, K., Suguna, K.

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references