6XVX

X-ray structure obtained upon reaction of dirhodium tetraacetate with RNase A (high resolution)

• PDB DOI: https://doi.org/10.2210/pdb6XVX/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2020-01-22 Released: 2020-02-19 
• Deposition Author(s): Merlino, A., Ferraro, G.
• Funding Organization(s): Italian Association for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.233 
• R-Value Work: 0.188 

Literature

Protein interactions of dirhodium tetraacetate: a structural study.

Ferraro, G., Pratesi, A., Messori, L., Merlino, A.

(2020) Dalton Trans 49: 2412-2416

• PubMed: 32022076 
• DOI: https://doi.org/10.1039/c9dt04819g
• Primary Citation of Related Structures:  
  6XVX, 6XW0


• PubMed Abstract: 
  

  The interactions between the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] and the model protein bovine pancreatic ribonuclease (RNase A) were investigated by high-resolution mass spectrometry and X-ray crystallography. The results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with RNase A. The metal compound binds the protein via coordination of the imidazole ring of a His side chain to one of its axial sites, while the dirhodium center and the acetato ligands remain unmodified. Data provide valuable information for the design of artificial dirhodium-containing metalloenzymes.

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Organizational Affiliation: 

Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia, 3-13, 50019, Sesto Fiorentino, Florence, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.24 kDa 
• Atom Count: 2,385 
• Modelled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A [auth AAA], B [auth BBB]	124	Bos taurus	Mutation(s): 0  EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RH3 (Subject of Investigation/LOI)	AA [auth BBB], K [auth AAA], L [auth AAA], M [auth AAA], N [auth AAA], X [auth BBB], Y [auth BBB], Z [auth BBB]	RHODIUM(III) ION Rh PZSJYEAHAINDJI-UHFFFAOYSA-N
ACT	C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], O [auth BBB], P [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB], T [auth BBB], U [auth BBB], V [auth BBB], W [auth BBB]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.233 
• R-Value Work: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.43	α = 90
b = 32.75	β = 90.38
c = 72.69	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Merlino, A., Ferraro, G.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	22578

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-03-04
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description