2B5Z

Hen lysozyme chemically glycosylated


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.212 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Production, crystallization and X-ray characterization of chemically glycosylated hen egg-white lysozyme.

Lopez-Jaramillo, F.J.Perez-Banderas, F.Hernandez-Mateo, F.Santoyo-Gonzalez, F.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 435-438

  • DOI: https://doi.org/10.1107/S1744309105008869
  • Primary Citation of Related Structures:  
    2B5Z

  • PubMed Abstract: 

    The crystallization of glycoproteins is one of the challenges to be confronted by the crystallographic community in the frame of what is known as glycobiology. The state of the art for the crystallization of glycoproteins is not promising and removal of the carbohydrate chains is generally suggested since they are flexible and a source of heterogeneity. In this paper, the feasibility of introducing glucose into the model protein hen egg-white lysozyme via a post-purification glycosylation reaction that may turn any protein into a model glycoprotein whose carbohydrate fraction can be manipulated is demonstrated.


  • Organizational Affiliation

    Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-UGRA, Facultad de Ciencias, Campus Fuentenueva, 18002 Granada, Spain. javier@lec.ugr.es


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGS
Query on BGS

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
(1S)-1,5-anhydro-1-(ethylsulfonyl)-D-glucitol
C8 H16 O7 S
OFMOVPVQFRZDRQ-CBQIKETKSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.58α = 90
b = 32.97β = 90
c = 120.27γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ProDCdata collection
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-03-27
    Changes: Database references