9EX1

X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure B)

• PDB DOI: https://doi.org/10.2210/pdb9EX1/pdb

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


• Deposited: 2024-04-05 Released: 2024-06-26 
• Deposition Author(s): Tito, G., Merlino, A., Ferraro, G.
• Funding Organization(s): Ministero dell Universita e della Ricerca

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.300 
• R-Value Work: 0.248 

Starting Model: experimental

Literature

Non-Covalent and Covalent Binding of New Mixed-Valence Cage-like Polyoxidovanadate Clusters to Lysozyme.

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

(2024) Angew Chem Int Ed Engl 63: e202406669-e202406669

• PubMed: 38842919 
• DOI: https://doi.org/10.1002/anie.202406669
• Primary Citation of Related Structures:  
  9EX0, 9EX1, 9EX2


• PubMed Abstract: 
  

  The high-resolution X-ray structures of the model protein lysozyme in the presence of the potential drug [VIVO(acetylacetonato)2] from crystals grown in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 reveal the binding to the protein of different and unexpected mixed-valence cage-like polyoxidovanadates (POVs): [V15O36(OH2)]5-, which non-covalently interacts with the lysozyme surface, [V15O33(OH2)]+ and [V20O51(OH2)]n- (this latter based on an unusual {V18O43} cage) which covalently bind the protein. EPR spectroscopy confirms the partial oxidation of VIV to VV and the formation of mixed-valence species. The results indicate that the interaction with proteins can stabilize the structure of unexpected - both for dimension and architecture - POVs, not observed in aqueous solution.

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Organizational Affiliation: 

University of Naples Federico II, Chemical Sciences, 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: 15.66 kDa 
• Atom Count: 1,091 
• Modelled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H8D (Subject of Investigation/LOI)	C [auth A]	Polyoxidovanadate complex O33 V15 DLKKHOPCDYTIQY-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.300 
• R-Value Work: 0.248 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.8	α = 90
b = 77.8	β = 90
c = 35.35	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: 2024-06-26 
Deposition Author(s): Tito, G., Merlino, A., Ferraro, G.

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Funding Organization	Location	Grant Number
Ministero dell Universita e della Ricerca	Italy	2022JMFC3X

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Structure summary
• Version 1.2: 2024-07-31
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Structure summary