9RBV | pdb_00009rbv

X-ray structure of lysozyme when is treated with Cs2[V(V)2O4(mal)2]2H2O at 310K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.293 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.218 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Speciation and structural transformation of a V V -malate complex in the absence and in the presence of a protein: from a dinuclear species to decavanadate.

Paolillo, M.Ferraro, G.Gumerova, N.I.Pisanu, F.Garribba, E.Rompel, A.Merlino, A.

(2025) Inorg Chem Front 12: 6503-6518

  • DOI: https://doi.org/10.1039/d5qi01384d
  • Primary Citation of Related Structures:  
    9RBG, 9RBT, 9RBV

  • PubMed Abstract: 

    A strategy for the development of new vanadium-based drugs is the preparation of complexes that target proteins and bear molecules involved in the cellular metabolism as ligands, like α-hydroxycarboxylic acids. Based on these premises, this study explores the solution behaviour of the dioxidovanadium(V) complex of malic acid, Cs 2 [V V 2 O 4 (mal) 2 ]·2H 2 O, and its interaction with the model protein lysozyme (HEWL) at room and at physiological temperature using 51 V nuclear magnetic resonance (NMR), electrospray ionisation-mass spectrometry (ESI-MS) and X-ray crystallography. The results show the coexistence in aqueous solution of various molecular species containing two or ten V V centres. In solution these species are formed regardless of the presence of HEWL, while at 37 °C the formation of [V V 10 O 28 ] 6- (V 10 ) is precluded when the protein is present. Crystallographic data reveal that, when protein crystals are incubated with the V compound at room temperature (25 °C) and at pH 4.0, [V IV O] 2+ , [V V 2 O 5 (mal)] 2- , [V V 10 O 26 ] 2- and [V V 10 O 28 ] 6- are bound to the protein, while at 37 °C, under the same conditions, only [V IV O] 2+ interacts with HEWL. [V V 10 O 28 ] 6- can bind the protein both covalently (as [V V 10 O 26 ] 2- ion) and non-covalently. Whereas the transformation of [V V 2 O 4 (mal) 2 ] 2- to [V V 2 O 5 (mal)] 2- is expected on the basis of thermodynamic considerations, the formation of V 10 and of the V 10 -HEWL adduct is not easily predictable. Docking calculations confirm the experimental results and highlight the role of protein-protein interaction in the stabilization of the revealed adduct. This study demonstrates that vanadium compounds can undergo transformation in solution, giving rise to species that interact with proteins through several binding modes and stabilization mechanisms.


  • Organizational Affiliation
    • Department of Chemical Sciences, University of Naples Federico II Complesso Universitario di Monte Sant'Angelo Via Cintia I-80126 Napoli Italy antonello.merlino@unina.it.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme CA [auth AAA]129Gallus gallusMutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.293 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.1α = 90
b = 79.1β = 90
c = 37.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references