6D9I

Pekin duck egg lysozyme isoform II (DEL-II)

• PDB DOI: https://doi.org/10.2210/pdb6D9I/pdb

• Classification: HYDROLASE
• Organism(s): Anas platyrhynchos
• Mutation(s): No 


• Deposited: 2018-04-30 Released: 2018-09-05 
• Deposition Author(s): Langley, D.B., Christ, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

Crystal structure of duck egg lysozyme isoform II (DEL-II).

Langley, D.B., Christ, D.

(2018) BMC Struct Biol 18: 10-10

• PubMed: 30134879 
• DOI: https://doi.org/10.1186/s12900-018-0090-7
• Primary Citation of Related Structures:  
  6D9I


• PubMed Abstract: 
  

  Lysozyme purified from duck eggs (DEL) has long been used as a model antigen as a counterpoint to the enzyme purified from hen eggs (HEL). However, unlike the single C-type variant found in hen eggs, duck eggs contain multiple isoforms: I, II and III. We recently reported the structures of isoforms I and III from Pekin duck (Anas platyrhynchos) and unequivocally determined the sequences of all three isoforms by mass spectrometry. Here we present the crystal structure of isoform II (DEL-II).

---

Organizational Affiliation: 

Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.22 kDa 
• Atom Count: 2,361 
• Modelled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A, B	129	Anas platyrhynchos	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00705 (Anas platyrhynchos) Explore P00705  Go to UniProtKB:  P00705

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.34	α = 90
b = 55.13	β = 95.95
c = 69.029	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Langley, D.B., Christ, D.

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description