4LYM

CRYSTAL STRUCTURE OF LOW HUMIDITY TETRAGONAL LYSOZYME AT 2.1-ANGSTROMS RESOLUTION. VARIABILITY IN HYDRATION SHELL AND ITS STRUCTURAL CONSEQUENCES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.162 

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This is version 1.5 of the entry. See complete history


Literature

Crystal structure of low humidity tetragonal lysozyme at 2.1-A resolution. Variability in hydration shell and its structural consequences.

Kodandapani, R.Suresh, C.G.Vijayan, M.

(1990) J Biol Chem 265: 16126-16131

  • DOI: https://doi.org/10.2210/pdb4lym/pdb
  • Primary Citation of Related Structures:  
    4LYM

  • PubMed Abstract: 

    Tetragonal crystals of hen egg white lysozyme undergo a reversible transformation, accompanied by loss of water, when the relative humidity of the environment is reduced to about 90%. The structure of the low humidity form has been analyzed, using x-ray data collected at 88% relative humidity, in order to explore the variability in protein hydration caused by a change in the amount of water surrounding the protein molecule and the consequent conformational perturbations in the molecule. The structure has been refined by the restrained least-squares method to an R value of 0.162 for 6269 observed reflections in the 10-2.1-A resolution shell. The refined structure provides interesting examples for the variability in helical parameters, the role of interactions involving side chains and water in the stabilization of secondary structural features, and favorable specific hydration sites. The protein molecule as a whole moves slightly in the low humidity form from its position in the native crystals. The hydration shell tends to move along with the protein. Significant changes, however, occur in the hydration shell. These changes cause structural perturbations in the enzyme molecule, which are most pronounced in regions involved in substrate binding.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEN EGG WHITE LYSOZYME129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.162 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.4α = 90
b = 78.4β = 90
c = 37.6γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.5: 2024-10-30
    Changes: Data collection, Database references, Structure summary