3MEH

Crystal structure of Staphylococcal nuclease variant Delta+PHS I92A at cryogenic temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Cavities determine the pressure unfolding of proteins.

Roche, J.Caro, J.A.Norberto, D.R.Barthe, P.Roumestand, C.Schlessman, J.L.Garcia, A.E.Garcia-Moreno E, B.Royer, C.A.

(2012) Proc.Natl.Acad.Sci.USA 109: 6945-6950

  • DOI: 10.1073/pnas.1200915109
  • Primary Citation of Related Structures:  3MHB, 3MVV, 3MXP, 3MZ5, 3NK9, 3NP8, 3NQT, 3NXW, 3OSO, 3R3O, 3PMF

  • PubMed Abstract: 
  • It has been known for nearly 100 years that pressure unfolds proteins, yet the physical basis of this effect is not understood. Unfolding by pressure implies that the molar volume of the unfolded state of a protein is smaller than that of the folded ...

    It has been known for nearly 100 years that pressure unfolds proteins, yet the physical basis of this effect is not understood. Unfolding by pressure implies that the molar volume of the unfolded state of a protein is smaller than that of the folded state. This decrease in volume has been proposed to arise from differences between the density of bulk water and water associated with the protein, from pressure-dependent changes in the structure of bulk water, from the loss of internal cavities in the folded states of proteins, or from some combination of these three factors. Here, using 10 cavity-containing variants of staphylococcal nuclease, we demonstrate that pressure unfolds proteins primarily as a result of cavities that are present in the folded state and absent in the unfolded one. High-pressure NMR spectroscopy and simulations constrained by the NMR data were used to describe structural and energetic details of the folding landscape of staphylococcal nuclease that are usually inaccessible with existing experimental approaches using harsher denaturants. Besides solving a 100-year-old conundrum concerning the detailed structural origins of pressure unfolding of proteins, these studies illustrate the promise of pressure perturbation as a unique tool for examining the roles of packing, conformational fluctuations, and water penetration as determinants of solution properties of proteins, and for detecting folding intermediates and other structural details of protein-folding landscapes that are invisible to standard experimental approaches.


    Organizational Affiliation

    Centre de Biochimie Structurale, Institut National pour la Santé et la Recherche Médicale U554, Centre National pour la Recherche Scientifique Unité Mixte de Recherche 5048, Université Montpellier 1&2, Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermonuclease
A
143Staphylococcus aureusGene Names: nuc
EC: 3.1.31.1
Find proteins for P00644 (Staphylococcus aureus)
Go to UniProtKB:  P00644
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: 1.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.090α = 90.00
b = 60.137β = 93.57
c = 38.194γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
CBASSdata collection
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

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: 2011-09-07
    Type: Atomic model
  • Version 1.3: 2012-05-23
    Type: Database references
  • Version 1.4: 2014-06-04
    Type: Atomic model
  • Version 1.5: 2017-11-08
    Type: Refinement description