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 

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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.,Sect.D 50: 250-257

  • DOI: 10.1107/S0907444993013290

  • 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 g ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEN EGG WHITE LYSOZYME
A, B
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.230α = 90.00
b = 63.660β = 92.90
c = 59.120γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1993-12-03 
  • Released Date: 1994-04-30 
  • Deposition Author(s): Harata, K.

Revision History 

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