3QOL

Crystal structure of Staphylococcal nuclease variant D+PHS/V23E at pH 6 determined at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein.

Robinson, A.C.Castaneda, C.A.Schlessman, J.L.Garcia-Moreno E, B.

(2014) Proc.Natl.Acad.Sci.USA 111: 11685-11690

  • DOI: 10.1073/pnas.1402900111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An artificial charge pair buried in the hydrophobic core of staphylococcal nuclease was engineered by making the V23E and L36K substitutions. Buried individually, Glu-23 and Lys-36 both titrate with pKa values near 7. When buried together their pKa v ...

    An artificial charge pair buried in the hydrophobic core of staphylococcal nuclease was engineered by making the V23E and L36K substitutions. Buried individually, Glu-23 and Lys-36 both titrate with pKa values near 7. When buried together their pKa values appear to be normal. The ionizable moieties of the buried Glu-Lys pair are 2.6 Å apart. The interaction between them at pH 7 is worth 5 kcal/mol. Despite this strong interaction, the buried Glu-Lys pair destabilizes the protein significantly because the apparent Coulomb interaction is sufficient to offset the dehydration of only one of the two buried charges. Save for minor reorganization of dipoles and water penetration consistent with the relatively high dielectric constant reported by the buried ion pair, there is no evidence that the presence of two charges in the hydrophobic interior of the protein induces any significant structural reorganization. The successful engineering of an artificial ion pair in a highly hydrophobic environment suggests that buried Glu-Lys pairs in dehydrated environments can be charged and that it is possible to engineer charge clusters that loosely resemble catalytic sites in a scaffold protein with high thermodynamic stability, without the need for specialized structural adaptations.


    Organizational Affiliation

    Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermonuclease
A
143Staphylococcus aureus (strain MW2)Mutation(s): 6 
Gene Names: nuc
EC: 3.1.31.1
Find proteins for Q8NXI6 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  Q8NXI6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
THP
Query on THP

Download SDF File 
Download CCD File 
A
THYMIDINE-3',5'-DIPHOSPHATE
C10 H16 N2 O11 P2
CSNCBOPUCJOHLS-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.033α = 90.00
b = 60.453β = 94.44
c = 37.626γ = 90.00
Software Package:
Software NamePurpose
XPREPdata reduction
PHASERphasing
REFMACrefinement
SAINTdata reduction
APEXdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-08-20
    Type: Database references
  • Version 1.3: 2014-09-03
    Type: Database references