4FYJ

Crystal Structure of P. aeruginosa peptidyl-tRNA hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa.

Hughes, R.C.McFeeters, H.Coates, L.McFeeters, R.L.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1472-1476

  • DOI: https://doi.org/10.1107/S1744309112045770
  • Primary Citation of Related Structures:  
    4FYJ

  • PubMed Abstract: 

    The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6(1)22 with unit-cell parameters a=b=63.62, c=155.20 Å, α=β=90, γ=120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da(-1). The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.


  • Organizational Affiliation

    Foresight Biosciences Inc., HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase199Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pthPA4672
EC: 3.1.1.29
UniProt
Find proteins for Q9HVC3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVC3 
Go to UniProtKB:  Q9HVC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVC3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.619α = 90
b = 63.619β = 90
c = 155.2γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.2: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description