7ZU6

Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to tetra-vanadate ion (structure 1)

• PDB DOI: https://doi.org/10.2210/pdb7ZU6/pdb

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


• Deposited: 2022-05-11 Released: 2023-05-24 
• Deposition Author(s): Tito, G., Merlino, A., Ferraro, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.196 
• R-Value Work: 0.171 

Literature

Stabilization and Binding of [V 4 O 12 ] 4- and Unprecedented [V 20 O 54 (NO 3 )] n- to Lysozyme upon Loss of Ligands and Oxidation of the Potential Drug V IV O(acetylacetonato) 2.

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

(2023) Angew Chem Int Ed Engl 62: e202310655-e202310655

• PubMed: 37768728 
• DOI: https://doi.org/10.1002/anie.202310655
• Primary Citation of Related Structures:  
  7ZU6, 8PTE


• PubMed Abstract: 
  

  High-resolution crystal structures of lysozyme in the presence of the potential drug V ^IV O(acetylacetonato) ₂ under two different experimental conditions have been solved. The crystallographic study reveals the loss of the ligands, the oxidation of V ^IV to V ^V and the subsequent formation of adducts of the protein with two different polyoxidovanadates: [V ₄ O ₁₂ ] ^4- , which interacts with lysozyme non-covalently, and the unprecedented [V ₂₀ O ₅₄ (NO ₃ )] ^n- , which is covalenty bound to the side chain of an aspartate residue of symmetry related molecules.

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Organizational Affiliation: 

Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, 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: 15.07 kDa 
• Atom Count: 1,298 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A [auth AAA]	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
V4O (Subject of Investigation/LOI)	D [auth AAA]	CYCLO-TETRAMETAVANADATE O12 V4 ACTPEXQBEHJTBO-UHFFFAOYSA-N
EPE	C [auth AAA]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
VVB (Subject of Investigation/LOI)	E [auth AAA]	bis(oxidanyl)vanadium H2 O2 V UVEFAEMXFFXFKB-UHFFFAOYSA-L
NA	B [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.196 
• R-Value Work: 0.171 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.05	α = 90
b = 77.05	β = 90
c = 37.84	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: 2023-05-24 
Deposition Author(s): Tito, G., Merlino, A., Ferraro, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references
• Version 1.2: 2023-12-13
  Changes: Database references
• Version 1.3: 2024-02-07
  Changes: Refinement description