1BB6

LYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOTRIOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 55: 60-66

  • DOI: 10.1107/S0907444998006623
  • Primary Citation of Related Structures:  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 ...

    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.,Sect.D 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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
129Oncorhynchus mykissEC: 3.2.1.17
Find proteins for P11941 (Oncorhynchus mykiss)
Go to UniProtKB:  P11941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMG
Query on UMG

Download SDF File 
Download CCD File 
A
METHYL-UMBELLIFERTL-N-ACETYL-CHITOTRIOSE
METHYLUMBELLIFERYL CHITOTRIOSE
C34 H47 N3 O18
BNYGKUQXGBVTRE-ITRNKESMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UMGKa: 500000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.690α = 90.00
b = 76.690β = 90.00
c = 54.710γ = 120.00
Software Package:
Software NamePurpose
CCP4phasing
SCALAdata scaling
PROLSQrefinement
CCP4model building
MADNESdata reduction
CCP4data scaling
MADNESdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance