4J1A | pdb_00004j1a

X-ray structure of the adduct between hen egg white lysozyme and AziRu (green crystal)

• PDB DOI: https://doi.org/10.2210/pdb4J1A/pdb

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


• Deposited: 2013-02-01 Released: 2013-04-03 
• Deposition Author(s): Vergara, A., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Interaction of Anticancer Ruthenium Compounds with Proteins: High-Resolution X-ray Structures and Raman Microscopy Studies of the Adduct between Hen Egg White Lysozyme and AziRu.

Vergara, A., D'Errico, G., Montesarchio, D., Mangiapia, G., Paduano, L., Merlino, A.

(2013) Inorg Chem 52: 4157-4159

• PubMed: 23517183 
• DOI: https://doi.org/10.1021/ic4004142
• Primary Citation Related Structures: 
  4J1A, 4J1B


• PubMed Abstract: 
  

  The binding properties of AziRu, a ruthenium(III) complex with high antiproliferative activity, toward a hen egg white lysozyme have been investigated by X-ray crystallography and Raman microscopy. The data provide clear evidence on the mechanism of AziRu-protein adduct formation and of ligand exchange in the crystal state.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 14.56 kDa 
• Atom Count: 1,230 
• Modeled Residue Count: 129 
• 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
RU	E [auth A]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
CL	B [auth A], C [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.189	α = 90
b = 78.189	β = 90
c = 37.157	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Vergara, A., Merlino, A.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-05-08
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary