2OE9

High-pressure structure of pseudo-WT T4 Lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography.

Collins, M.D.Quillin, M.L.Hummer, G.Matthews, B.W.Gruner, S.M.

(2007) J.Mol.Biol. 367: 752-763

  • DOI: 10.1016/j.jmb.2006.12.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded ...

    Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded states. To gain a more complete picture requires that we perturb these structures in a continuous manner, something mutagenesis cannot achieve. With high pressure crystallographic methods it is now possible to explore the detailed properties of proteins while continuously varying thermodynamic parameters. Here, we detail the structural response of the cavity-containing mutant L99A of T4 lysozyme, as well as its pseudo wild-type (WT*) counterpart, to hydrostatic pressure. Surprisingly, the cavity has almost no effect on the pressure response: virtually the same changes are observed in WT* as in L99A under pressure. The cavity is most rigid, while other regions deform substantially. This implies that while some residues may increase the thermodynamic stability of a protein, they may also be structurally irrelevant. As recently shown, the cavity fills with water at pressures above 100 MPa while retaining its overall size. The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone.


    Related Citations: 
    • Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
      Collins, M.D.,Quillin, M.L.,Hummer, G.,Matthews, B.M.,Gruner, S.M.
      (2005) Proc.Natl.Acad.Sci.USA 102: 16668


    Organizational Affiliation

    Department of Physics, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
X
164Enterobacteria phage T4Mutation(s): 2 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
X
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.554α = 90.00
b = 60.554β = 90.00
c = 95.567γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description