2RJT

Crystal Structure Analysis of a Surface Entropy Reduction Mutant of S. pneumoniae FabF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Surface-entropy reduction approaches to manipulate crystal forms of beta-ketoacyl acyl carrier protein synthase II from Streptococcus pneumoniae.

Parthasarathy, G.Cummings, R.Becker, J.W.Soisson, S.M.

(2008) Acta Crystallogr.,Sect.D 64: 141-148

  • DOI: 10.1107/S090744490705559X

  • PubMed Abstract: 
  • A series of experiments with beta-ketoacyl acyl carrier protein synthase II (FabF) from Streptococcus pneumonia (spFabF) were undertaken to evaluate the capability of surface-entropy reduction (SER) to manipulate protein crystallization. Previous wor ...

    A series of experiments with beta-ketoacyl acyl carrier protein synthase II (FabF) from Streptococcus pneumonia (spFabF) were undertaken to evaluate the capability of surface-entropy reduction (SER) to manipulate protein crystallization. Previous work has shown that this protein crystallizes in two forms. The triclinic form contains four molecules in the asymmetric unit (a.u.) and diffracts to 2.1 A resolution, while the more desirable primitive orthorhombic form contains one molecule in the a.u. and diffracts to 1.3 A. The aim was to evaluate the effect of SER mutations that were specifically engineered to avoid perturbing the crystal-packing interfaces employed by the favorable primitive orthorhombic crystal form while potentially disrupting a surface of the protein employed by the less desirable triclinic crystal form. Two mutant proteins were engineered, each of which harbored five SER mutations. Extensive crystallization screening produced crystals of the two mutants, but only under conditions that differed from those used for the native protein. One of the mutant proteins yielded crystals that were of a new form (centered orthorhombic), despite the fact that the interfaces employed by the primitive orthorhombic form of the native protein were specifically unaltered. Structure determination at 1.75 A resolution reveals that one of the mutations, E383A, appears to play a key role in disfavouring the less desirable triclinic crystal form and in generating a new surface for a packing interaction that stabilizes the new crystal form.


    Organizational Affiliation

    Merck Research Laboratories, Rahway, NJ, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-ketoacyl-ACP synthase II
A, D, C, B
428Streptococcus pneumoniaeMutation(s): 5 
Gene Names: fabF (fabF_1, fabF_2, fabF_3)
EC: 2.3.1.179
Find proteins for Q9FBC2 (Streptococcus pneumoniae)
Go to UniProtKB:  Q9FBC2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 112.417α = 90.00
b = 115.872β = 90.00
c = 278.923γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
TNTrefinement
ADSCdata collection
DENZOdata reduction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Refinement description