1LYS

X-RAY STRUCTURE OF A MONOCLINIC FORM OF HEN EGG-WHITE LYSOZYME CRYSTALLIZED AT 313K. COMPARISON OF TWO INDEPENDENT MOLECULES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history


Literature

X-ray structure of a monoclinic form of hen egg-white lysozyme crystallized at 313 K. Comparison of two independent molecules.

Harata, K.

(1994) Acta Crystallogr D Biol Crystallogr 50: 250-257

  • DOI: https://doi.org/10.1107/S0907444993013290
  • Primary Citation of Related Structures:  
    1LYS

  • PubMed Abstract: 

    A monoclinic crystal of hen egg lysozyme (HEL, E.C. 3.2.1.17) was obtained at 313 K from a 10%(w/v) NaCl solution at pH 7.6 containing 5%(v/v) 1-propanol. Cell dimensions were a = 27.23, b = 63.66, c = 59.12 A and beta = 92.9 degrees, and the space group was P2(1). The unit cell contains four molecules (V(m) = 1.79 A(3) Da(-1)). The structure was solved by the isomorphous replacement method with anomalous scattering followed by phase improvement by the solvent-flattening method. The refinement of the structure was carried out by the simulated-annealing method. The conventional R value was 0.187 for 18 260 reflections [|F(o)| > 3sigma(F)] in the resolution range 10-1.72 A. The r.m.s. deviations from the ideal bond distances and angles were 0.015 A and 3.0 degrees, respectively. The two molecules in the asymmetric unit are related by a translation of half a lattice unit along the a and c axes. The r.m.s. difference of equivalent C(alpha) atoms between the two molecules was 0.64 A and the largest difference was 3.57 A for Gly71. A significant structural change was observed in the regions of residues 45-50, 65-73 and 100-104. The residues 45-50, which connect two beta-strands, are shifted parallel to the beta-sheet plane between the two molecules. The residues 100-104 belong to the substrate-binding site (subsite A) and the high flexibility of this region may be responsible for the binding of the substrate and the release of reaction products.


  • Organizational Affiliation

    Biomolecules Department, National Institute of Bioscience and Human Technology, Tsukuba, Ibaraki, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEN EGG WHITE LYSOZYME
A, B
129Gallus 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: 1.72 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.23α = 90
b = 63.66β = 92.9
c = 59.12γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 1994-04-30 
  • Deposition Author(s): Harata, K.

Revision History  (Full details and data files)

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other