4PRQ

CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH SCLX4 AT 1.72 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb4PRQ/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-06 Released: 2014-09-10 
• Deposition Author(s): McGovern, R.E., McCarthy, A.A., Crowley, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.222 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Protein assembly mediated by sulfonatocalix[4]arene.

McGovern, R.E., McCarthy, A.A., Crowley, P.B.

(2014) Chem Commun (Camb) 50: 10412-10415

• PubMed: 25068633 
• DOI: https://doi.org/10.1039/c4cc04897k
• Primary Citation of Related Structures:  
  4PRQ


• PubMed Abstract: 
  

  A crystal structure of lysozyme in complex with p-sulfonato-calix[4]arene (sclx4) reveals a linear assembly of protein tetramers glued together by protein-calixarene interactions. One interaction involves encapsulation of the highly exposed C-terminal Arg128. The other involves an intricate protein-bound complex of sclx4, Mg(2+) and a fragment of polyethylene glycol.

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Organizational Affiliation: 

School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.25 kDa 
• Atom Count: 4,664 
• Modelled Residue Count: 516 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T3Y	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid C28 H24 O16 S4 JFYBCAFLVNKHHG-UHFFFAOYSA-N
P6G	H [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG6	N [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4	G [auth A], L [auth B], M [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	O [auth B], P [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.222 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.01	α = 90
b = 81.749	β = 105.37
c = 72.1	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): McGovern, R.E., McCarthy, A.A., Crowley, P.B.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary