2B6Z

T4 Lysozyme mutant L99A at ambient pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation

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

(2005) Proc Natl Acad Sci U S A 102: 16668-16671

  • DOI: https://doi.org/10.1073/pnas.0508224102
  • Primary Citation of Related Structures:  
    2B6W, 2B6X, 2B6Y, 2B6Z, 2B70, 2B72, 2B73, 2B74, 2B75, 2OE4

  • PubMed Abstract: 

    Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in "hydrophobic" cavities is required for the function of some proteins. Hydration of the protein core has also been suggested as the mechanism of pressure-induced unfolding. We therefore are led to ask whether even the most nonpolar protein core is truly hydrophobic (i.e., water-repelling). To answer this question we probed the hydration of an approximately 160-A(3), highly hydrophobic cavity created by mutation in T4 lysozyme by using high-pressure crystallography and molecular dynamics simulation. We show that application of modest pressure causes approximately four water molecules to enter the cavity while the protein itself remains essentially unchanged. The highly cooperative filling is primarily due to a small change in bulk water activity, which implies that changing solvent conditions or, equivalently, cavity polarity can dramatically affect interior hydration of proteins and thereby influence both protein activity and folding.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme162Tequatrovirus T4Mutation(s): 3 
Gene Names: E
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00720
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.954α = 90
b = 60.954β = 90
c = 96.607γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Adxvdata processing
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection