5JVX | pdb_00005jvx

X-ray structure of the adduct formed in the reaction between thaumatin and a gold carbene compound

• PDB DOI: https://doi.org/10.2210/pdb5JVX/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Mutation(s): No 


• Deposited: 2016-05-11 Released: 2016-07-13 
• Deposition Author(s): Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.187 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

First Crystal Structure for a Gold Carbene-Protein Adduct.

Ferraro, G., Gabbiani, C., Merlino, A.

(2016) Bioconjug Chem 27: 1584-1587

• PubMed: 27364343 
• DOI: https://doi.org/10.1021/acs.bioconjchem.6b00298
• Primary Citation Related Structures: 
  5JVX


• PubMed Abstract: 
  

  The X-ray structure of the adduct formed in the reaction between the gold N-heterocyclic carbene compound Au(NHC)Cl (with NHC = 1-butyl-3-methyl-imidazole-2-ylidene) and the model protein thaumatin is reported here. The structure reveals binding of Au(NHC)(+) fragments to distinct protein sites. Notably, binding of the gold compound occurs at lysine side chains and at the N-terminal tail; the metal binds the protein after releasing Cl(-) ligand, but retaining NHC fragment.

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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.
Department of Chemistry and Industrial Chemistry, University of Pisa , Via Moruzzi 13, 56124 Pisa, 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: 24.79 kDa 
• Atom Count: 2,020 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin-1	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6O0	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	(1-butyl-3-methyl-1,3-dihydro-2H-imidazol-2-ylidene)(chloro)gold C8 H14 Au Cl N2 VPJMTYLCIKLAAU-UHFFFAOYSA-M
TLA	B [auth A], C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.187 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.912	α = 90
b = 57.912	β = 90
c = 150.136	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary