4PRQ

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

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
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Protein assembly mediated by sulfonatocalix[4]arene.

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

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

  • 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.

    • Organizational Affiliation: 

    School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland. [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C
A, B, C, D
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3Y
Query on T3Y
Download Ideal Coordinates CCD File 
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
Query on P6G
Download Ideal Coordinates CCD File 
H [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG6
Query on PG6
Download Ideal Coordinates CCD File 
N [auth B]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4
Query on PG4
Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
M [auth B]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
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 = 44.01α = 90
b = 81.749β = 105.37
c = 72.1γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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