2RHS

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Rational protein engineering in action: the first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus.

Evdokimov, A.G.Mekel, M.Hutchings, K.Narasimhan, L.Holler, T.McGrath, T.Beattie, B.Fauman, E.Yan, C.Heaslet, H.Walter, R.Finzel, B.Ohren, J.McConnell, P.Braden, T.Sun, F.Spessard, C.Banotai, C.Al-Kassim, L.Ma, W.Wengender, P.Kole, D.Garceau, N.Toogood, P.Liu, J.

(2008) J Struct Biol 162: 152-169

  • DOI: https://doi.org/10.1016/j.jsb.2007.11.002
  • Primary Citation of Related Structures:  
    2RHQ, 2RHS

  • PubMed Abstract: 

    In this article, we describe for the first time the high-resolution crystal structure of a phenylalanine tRNA synthetase from the pathogenic bacterium Staphylococcus haemolyticus. We demonstrate the subtle yet important structural differences between this enzyme and the previously described Thermus thermophilus ortholog. We also explain the structure-activity relationship of several recently reported inhibitors. The native enzyme crystals were of poor quality--they only diffracted X-rays to 3-5A resolution. Therefore, we have executed a rational surface mutagenesis strategy that has yielded crystals of this 2300-amino acid multidomain protein, diffracting to 2A or better. This methodology is discussed and contrasted with the more traditional domain truncation approach.


  • Organizational Affiliation

    Pfizer Global Research & Development, Michigan Laboratories, Ann Arbor, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. artem@xtals.org


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase alpha chain
A, C
294Staphylococcus haemolyticusMutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
UniProt
Find proteins for Q4L5E3 (Staphylococcus haemolyticus (strain JCSC1435))
Explore Q4L5E3 
Go to UniProtKB:  Q4L5E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4L5E3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase beta chain
B, D
800Staphylococcus haemolyticusMutation(s): 5 
Gene Names: pheT
EC: 6.1.1.20
UniProt
Find proteins for Q4L5E4 (Staphylococcus haemolyticus (strain JCSC1435))
Explore Q4L5E4 
Go to UniProtKB:  Q4L5E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4L5E4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.714α = 90
b = 87.861β = 90.59
c = 234.036γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-21
    Changes: Data collection