1BB6

LYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOTRIOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 

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: 10.1107/S0907444998006623
  • Primary Citation of Related Structures:  
    1BB7, 1BB6

  • 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 ...

    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.


    Related Citations: 
    • Crystal Structures of Three Complexes between Chito-Oligosaccharides and Lysozyme from the Rainbow Trout. How Distorted is the Nag Sugar in Site D?
      Karlsen, S., Hough, E.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 962
    • Refined Crystal Structure of Lysozyme from the Rainbow Trout (Oncorhynchus Mykiss)
      Karlsen, S., Eliassen, B.E., Hansen, L.K., Larsen, R.L., Riise, B.W., Smalas, A.O., Hough, E., Grinde, B.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 354

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA129Oncorhynchus mykissMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P11941 (Oncorhynchus mykiss)
Explore P11941 
Go to UniProtKB:  P11941
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMG
Query on UMG

Download Ideal Coordinates CCD File 
B [auth A]METHYL-UMBELLIFERTL-N-ACETYL-CHITOTRIOSE
C34 H47 N3 O18
BNYGKUQXGBVTRE-ITRNKESMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UMGKa:  500000   M^-1  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.69α = 90
b = 76.69β = 90
c = 54.71γ = 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