1SF6

BINDING OF N,N',N"-TRIACETYLCHITOTRIOSE TO HEW LYSOZYME: A POWDER DIFFRACTION STUDY


Experimental Data Snapshot

ERROR: Experimental Data Snapshots data not found.

wwPDB Validation

Currently 1SF6 does not have a wwPDB validation report.


This is version 1.2 of the entry. See complete history

Literature

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

Von Dreele, R.B.

(2005) Acta Crystallogr.,Sect.D 61: 22-32

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

  • PubMed Abstract: 
  • The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC 3.2.1.17) 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 3.2.1.17) 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: 
    • Binding of N-Acetylglucoasmine to Chicken Egg Lysozyme: A Powder Diffraction Study
      Von Dreele, R.B.
      (2001) Acta Crystallogr.,Sect.D 57: 1836
    • 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.,Sect.D 56: 1549
    • Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure
      Von Dreele, R.B.
      (1999) J.Appl.Crystallogr. 32: 1084


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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

ERROR: Experimental Data Snapshots data not found.
Software Package:
Software NamePurpose
GSASmodel building
povdata collection
POVdata reduction
GSASphasing
GSASrefinement
PROCESSdata reduction
PROCESSdata scaling

Structure Validation

Currently 1SF6 does not have a wwPDB 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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance