9I8L | pdb_00009i8l

X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2</sub>] at 310 K

• PDB DOI: https://doi.org/10.2210/pdb9I8L/pdb

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


• Deposited: 2025-02-05 Released: 2025-05-14 
• Deposition Author(s): Tito, G., Ferraro, G., Merlino, A.
• Funding Organization(s): NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.284 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.207 (DCC) 

Starting Model: experimental

Literature

Formation of Mixed-Valence Cage-Like Polyoxidovanadates at 37°C Upon Reaction of V IV O(acetylacetonato) 2 With Lysozyme.

Tito, G., Ferraro, G., Garribba, E., Merlino, A.

(2025) Chemistry 31: e202500488-e202500488

• PubMed: 40271720 
• DOI: https://doi.org/10.1002/chem.202500488
• Primary Citation of Related Structures:  
  9I8L


• PubMed Abstract: 
  

  Crystals of the model protein lysozyme were grown and soaked with the potential drug VIVO(acetylacetonato)2 at 37°C. X-ray diffraction and electron paramagnetic resonance data collected at this temperature reveal that mixed-valence cage-like polyoxidovanadate clusters are formed and covalently bind protein residue side chains at physiological temperature.

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Organizational Affiliation: 
• University of Naples Federico II: Universita degli Studi di Napoli Federico II, Chemical Sciences, ITALY.
Università degli Studi di Sassari: Universita degli Studi di Sassari, Dipartimento di Medicina, Chirurgia e Farmacia, ITALY.
University of Naples 'Federico II', Dept. of Chemical Sciences, via cintia, I-80126, Napoli, ITALY.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.52 kDa 
• Atom Count: 1,171 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ICR (Subject of Investigation/LOI)	D [auth A]	Polyoxidovanadate complex O51 V20 UMGUOOQNHDXOEA-UHFFFAOYSA-N
A1H8D (Subject of Investigation/LOI)	E [auth A]	Polyoxidovanadate complex O33 V15 DLKKHOPCDYTIQY-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.284 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.207 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.86	α = 90
b = 80.86	β = 90
c = 36.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Tito, G., Ferraro, G., Merlino, A.

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Funding Organization	Location	Grant Number
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)	Italy	2022JMFC3X
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)	Italy	2022APCTNA

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references
• Version 1.2: 2025-06-18
  Changes: Database references