3TD2

Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 5

• PDB DOI: https://doi.org/10.2210/pdb3TD2/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-10 Released: 2012-02-15 
• Deposition Author(s): Selvaraj, M., Ahmad, R., Varshney, U., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.255 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 

Literature

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

Selvaraj, M., Ahmad, R., Varshney, U., Vijayan, M.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 124-128

• PubMed: 22297982 
• DOI: https://doi.org/10.1107/S1744309111052341
• Primary Citation of Related Structures:  
  3TCK, 3TCN, 3TD2, 3TD6


• PubMed Abstract: 
  

  The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M. tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.49 kDa 
• Atom Count: 1,435 
• Modelled Residue Count: 187 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	191	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: MT1042, MTCY10G2.35, pth, Rv1014c EC: 3.1.1.29
UniProt
Find proteins for P9WHN7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHN7  Go to UniProtKB:  P9WHN7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.255 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.31	α = 90
b = 60.31	β = 90
c = 87.67	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Selvaraj, M., Ahmad, R., Varshney, U., Vijayan, M.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description