1LZY

X-RAY STRUCTURE OF TURKEY EGG LYSOZYME COMPLEX WITH DI-N-ACETYLCHITOBIOSE. RECOGNITION AND BINDING OF ALPHA-ANOMERIC FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution.

Harata, K.

(1993) Acta Crystallogr.,Sect.D 49: 497-504

  • DOI: 10.1107/S0907444993005542
  • Primary Citation of Related Structures:  
  • Also Cited By: 1XFT

  • PubMed Abstract: 
  • Monoclinic crystals of turkey egg lysozyme (TEL, E.C. 3.2.1.17) were obtained from 2.2 M ammonium sulfate solution at pH 4.2. They belong to space group P2(1) with unit-cell dimensions a = 38.07, b = 33.20, c = 46.12 A and beta = 110.1 degrees, and c ...

    Monoclinic crystals of turkey egg lysozyme (TEL, E.C. 3.2.1.17) were obtained from 2.2 M ammonium sulfate solution at pH 4.2. They belong to space group P2(1) with unit-cell dimensions a = 38.07, b = 33.20, c = 46.12 A and beta = 110.1 degrees, and contain one molecule in the asymmetric unit (V(m) = 1.91 A(3) Da(-1)). The three-dimensional structure of TEL was solved by the method of multiple isomorphous replacement with anomalous scattering. Area detector data to 1.5 A resolution from native and heavy-atom derivatives were used for the structure determination. The structure was refined by the simulated-annealing method with diffraction data of 10-1.30 A resolution. The conventional R factor was 0.189. The root-mean-square deviations from ideal bond distances and angles were 0.016 A and 2.9 degrees, respectively. The backbone structure of TEL is very similar to that of hen egg lysozyme (HEL) and the difference in seven amino-acid residues does not affect the basic folding of the polypeptide chain. Except for the region from Gly101 to Gly104, the geometry of the active-site cleft is conserved between TEL and HEL. The Gly101 residue is located at the end of the sugar-binding site and the structural change in this region between TEL and HEL is considered to be responsible for the difference in their enzymatic properties.


    Related Citations: 
    • X-Ray Structure of Monoclinic Turkey Egg Lysozyme at 1.3 Angstroms Resolution
      Harata, K.
      (1993) Acta Crystallogr.,Sect.D 49: 497


    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
TURKEY EGG WHITE LYSOZYME
A
129Meleagris gallopavoMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00703 (Meleagris gallopavo)
Go to Gene View: LYZ
Go to UniProtKB:  P00703
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.220α = 90.00
b = 33.140β = 109.90
c = 46.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-01-09 
  • Released Date: 1995-02-27 
  • Deposition Author(s): Harata, K.

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other