1BB7

LYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOBIOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural studies on the binding of 4-methylumbelliferone glycosides of chitin to rainbow trout lysozyme.

Vollan, V.B.Hough, E.Karlsen, S.

(1999) Acta Crystallogr D Biol Crystallogr 55: 60-66

  • DOI: https://doi.org/10.1107/S0907444998006623
  • Primary Citation of Related Structures:  
    1BB6, 1BB7

  • PubMed Abstract: 

    Two complexes between rainbow trout lysozyme (RBTL) and 4-methylumbelliferyl chitobioside, 4MeU-(GlcNAc)2, and chitotrioside, 4MeU-(GlcNAc)3, were produced by co-crystallization and soaking, respectively, and the crystal structures were solved at 2.0 A resolution. The results show that 4-MeU-(GlcNAc)3 binds in subsites A-D and that 4-MeU-(GlcNAc)2 binds in subsites B-D in the active-site cleft of RBTL. This agrees well with earlier crystallographic studies on the binding of oligosaccharides of chitin to RBTL, which showed that (GlcNAc)3 binds to sites B-D in RBTL and not to A-C as seen in the human and turkey egg-white lysozymes. For both complexes the 4-MeU moiety in site D has diffuse electron density and is flexible, as it is only bound to water molecules and not to the protein. Since no electron density was observed in site E, the solved structures give views of nonproductive enzyme-substrate complexes.


  • Organizational Affiliation

    Protein Crystallography Group, Department of Chemistry, Faculty of Science, University of Tromso, N-9037 Tromso, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOZYME129Oncorhynchus mykissMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P11941 (Oncorhynchus mykiss)
Explore P11941 
Go to UniProtKB:  P11941
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11941
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GUM
Query on GUM

Download Ideal Coordinates CCD File 
B [auth A]4-METHYL-UMBELLIFERYL-N-ACETYL-CHITOBIOSE
C26 H34 N2 O13
UPSFMJHZUCSEHU-JYGUBCOQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.42α = 90
b = 76.42β = 90
c = 54.19γ = 120
Software Package:
Software NamePurpose
MADNESdata collection
SCALAdata scaling
CCP4model building
PROLSQrefinement
MADNESdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-04
    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: 2018-04-18
    Changes: Data collection