Experimental Data Snapshot


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Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study.

Von Dreele, R.B.

(2005) Acta Crystallogr D Biol Crystallogr 61: 22-32

  • DOI: 10.1107/S0907444904025715
  • Primary Citation of Related Structures:  
    1SF7, 1SF6, 1SF4, 1SFB, 1SFG

  • PubMed Abstract: 
  • The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitatio ...

    The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitation preparations in 1.0 M NaCl pH 6.0 buffer. The location of each NAGn was easily found from difference Fourier maps generated from structure factors extracted during preliminary Rietveld refinements. Full NAGn-protein structures were subjected to combined Rietveld and stereochemical restraint refinements (Rwp = 2.28-2.59%; Rp = 1.81-2.04%; RF2 = 3.91-5.80%) and revealed binding modes for NAGn that depended on the length of the NAG oligosaccharide. The NAG2 ligand was found in the BC sites in the cleft of HEWL, NAG3 was found to bind in both the ABC and BCD sites in the ratio 35:65 and NAG4 and NAG5 bound to the ABCD and ABCDE sites, respectively, while NAG6 only bound to sites ABCDE, leaving the F site empty with the remaining saccharide ring located in a solvent region adjacent to the A site. All protein powder diffraction patterns in this study consisted of extremely sharp Bragg peaks consistent with approximately 1 microm crystallites that were devoid of line-broadening defects. Details of the stereochemical restraints used in these refinements and their impact on structural validation are also discussed.

    Related Citations: 
    • Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure
      Von Dreele, R.B.
      (1999) J Appl Crystallogr 32: 1084
    • The First Protein Crystal Structure Determined from High Resolution X-Ray Powder Diffraction Data: A Variant of the T3R3 Human Insulin Zinc Complex Produced by Grinding
      Von Dreele, R.B., Stephens, P.W., Blessing, R.H., Smith, G.D.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 1549
    • Binding of N-Acetylglucoasmine to Chicken Egg Lysozyme: A Powder Diffraction Study
      Von Dreele, R.B.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 1836

    Organizational Affiliation

    XPS/IPNS Divisions, Argonne National Laboratory, Argonne, IL 60439, USA. vondreele@anl.gov

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
  • Reference Sequence


Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
4 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.77α = 90
b = 78.77β = 90
c = 38.368γ = 90
Software Package:
Software NamePurpose
povdata collection
PROCESSdata reduction
GSASmodel building
POVdata reduction
PROCESSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Deposited Date: 2004-02-19 
  • Released Date: 2004-03-02 
  • Deposition Author(s): Von Dreele, R.B.

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary