5V94 | pdb_00005v94

Pekin duck egg lysozyme isoform III (DEL-III), cubic form

• PDB DOI: https://doi.org/10.2210/pdb5V94/pdb

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


• Deposited: 2017-03-22 Released: 2017-11-15 
• Deposition Author(s): Langley, D.B., Christ, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.214 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structural basis of antigen recognition: crystal structure of duck egg lysozyme.

Langley, D.B., Crossett, B., Schofield, P., Jackson, J., Zeraati, M., Maltby, D., Christie, M., Burnett, D., Brink, R., Goodnow, C., Christ, D.

(2017) Acta Crystallogr D Struct Biol 73: 910-920

• PubMed: 29095163 
• DOI: https://doi.org/10.1107/S2059798317013730
• Primary Citation Related Structures: 
  5V8G, 5V92, 5V94, 5VAS


• PubMed Abstract: 
  

  Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.

---

Organizational Affiliation: 
• Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.
The Mass Spectrometry Core Facility, The University of Sydney, The Hub, Charles Perkins Centre, Building D17, Camperdown, NSW 2006, Australia.
Molecular, Structural and Computational Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW 2010, Australia.

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: 30.16 kDa 
• Atom Count: 2,182 
• Modeled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lysozyme isoform III	A, B	129	Anas platyrhynchos	Mutation(s): 0  EC: 3.2.1.18 (PDB Primary Data), 3.2.1.17 (UniProt)
UniProt
Find proteins for P00705 (Anas platyrhynchos) Explore P00705  Go to UniProtKB:  P00705

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MRD	H [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
PO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.214 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

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

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Langley, D.B., Christ, D.

---

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2018-05-09
  Changes: Data collection, Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary