2OXP

Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal asp

Karp, D.A.Gittis, A.G.Stahley, M.R.Fitch, C.A.Stites, W.E.Garcia-Moreno, E.B.

(2007) Biophys.J. 92: 2041-2053

  • DOI: 10.1529/biophysj.106.090266

  • PubMed Abstract: 
  • The dielectric properties of proteins are poorly understood and difficult to describe quantitatively. This limits the accuracy of methods for structure-based calculation of electrostatic energies and pK(a) values. The pK(a) values of many internal gr ...

    The dielectric properties of proteins are poorly understood and difficult to describe quantitatively. This limits the accuracy of methods for structure-based calculation of electrostatic energies and pK(a) values. The pK(a) values of many internal groups report apparent protein dielectric constants of 10 or higher. These values are substantially higher than the dielectric constants of 2-4 measured experimentally with dry proteins. The structural origins of these high apparent dielectric constants are not well understood. Here we report on structural and equilibrium thermodynamic studies of the effects of pH on the V66D variant of staphylococcal nuclease. In a crystal structure of this protein the neutral side chain of Asp-66 is buried in the hydrophobic core of the protein and hydrated by internal water molecules. Asp-66 titrates with a pK(a) value near 9. A decrease in the far UV-CD signal was observed, concomitant with ionization of this aspartic acid, and consistent with the loss of 1.5 turns of alpha-helix. These data suggest that the protein dielectric constant needed to reproduce the pK(a) value of Asp-66 with continuum electrostatics calculations is high because the dielectric constant has to capture, implicitly, the energetic consequences of the structural reorganization that are not treated explicitly in continuum calculations with static structures.


    Organizational Affiliation

    Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermonuclease
A
149Staphylococcus aureus (strain MW2)Mutation(s): 3 
Gene Names: nuc
EC: 3.1.31.1
Find proteins for Q8NXI6 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  Q8NXI6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 47.579α = 90.00
b = 47.579β = 90.00
c = 62.791γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance