2RHQ

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jsb.2007.11.002
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase beta chainB795Staphylococcus haemolyticusMutation(s): 6 
Gene Names: pheT
EC: 6.1.1.20
Find proteins for Q4L5E4 (Staphylococcus haemolyticus (strain JCSC1435))
Explore Q4L5E4 
Go to UniProtKB:  Q4L5E4
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase alpha chainA294Staphylococcus haemolyticusMutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
Find proteins for Q4L5E3 (Staphylococcus haemolyticus (strain JCSC1435))
Explore Q4L5E3 
Go to UniProtKB:  Q4L5E3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAX
Query on GAX

Download CCD File 
A
1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea
C19 H20 N6 O3 S2
NJPVZSIGDRLLTD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 249.312α = 90
b = 87.602β = 100.44
c = 61.072γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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