4C3W | pdb_00004c3w

Vanadium(IV)-Picolinate Complexed with Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb4C3W/pdb

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


• Deposited: 2013-08-28 Released: 2014-07-09 
• Deposition Author(s): Santos, M.F.A., Correia, I., Oliveira, A.R., Garribba, E., Pessoa, J.C., Romao, M.J., Santos-Silva, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Vanadium Complexes as Prospective Therapeutics: Structural Characterization of a V(Iv) Lysozyme Adduct

Santos, M.F.A., Correia, I., Oliveira, A.R., Garribba, E., Pessoa, J.C., Santos-Silva, T.

(2014) Eur J Inorg Chem 21: 3293

• DOI: https://doi.org/10.1002/EJIC.201402408

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: 14.81 kDa 
• Atom Count: 1,200 
• 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
AIV	B [auth A]	hydroxy(oxo)bis(pyridine-2-carboxylato-kappa~2~N,O)vanadium(3+) C12 H9 N2 O6 V MPIJUROFANKBHX-UHFFFAOYSA-K
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.12	α = 90
b = 78.12	β = 90
c = 37.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Santos, M.F.A., Correia, I., Oliveira, A.R., Garribba, E., Pessoa, J.C., Romao, M.J., Santos-Silva, T.

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-08-27
  Changes: Database references
• Version 1.2: 2014-09-03
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-10-23
  Changes: Structure summary