1BB7 | pdb_00001bb7

LYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOBIOSE


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 1BB7

This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 14.89 kDa 
  • Atom Count: 1,173 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor) 
  • R-Value Work:  0.175 (Depositor) 
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
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary