2B5Z | pdb_00002b5z

Hen lysozyme chemically glycosylated

• PDB DOI: https://doi.org/10.2210/pdb2B5Z/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2005-09-29 Released: 2006-10-03 
• Deposition Author(s): Lopez-Jaramillo, F.J., Perez-Balderas, F., Hernandez-Mateo, F., Santoyo-Gonzalez, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.211 (DCC) 

Starting Model: experimental

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

• PubMed: 16511062 
• DOI: https://doi.org/10.1107/S1744309105008869
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-UGRA, Facultad de Ciencias, Campus Fuentenueva, 18002 Granada, Spain. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.57 kDa 
• Atom Count: 1,148 
• Modeled Residue Count: 127 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGS	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	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI	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 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.211 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.58	α = 90
b = 32.97	β = 90
c = 120.27	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ProDC	data collection
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Lopez-Jaramillo, F.J., Perez-Balderas, F., Hernandez-Mateo, F., Santoyo-Gonzalez, F.

Revision History  

• 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
• Version 1.7: 2024-10-30
  Changes: Structure summary