5JMG

X-ray structure of the complex between bovine pancreatic ribonuclease and pentachlorocarbonyliridate(III) (4 days of soaking)

• PDB DOI: https://doi.org/10.2210/pdb5JMG/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2016-04-29 Released: 2016-07-27 
• Deposition Author(s): Caterino, M., Petruk, A.A., Vergara, A., Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules.

Caterino, M., Petruk, A.A., Vergara, A., Ferraro, G., Marasco, D., Doctorovich, F., Estrin, D.A., Merlino, A.

(2016) Dalton Trans 45: 12206-12214

• PubMed: 27411388 
• DOI: https://doi.org/10.1039/c6dt01685e
• Primary Citation of Related Structures:  
  5JMG, 5JML


• PubMed Abstract: 
  

  A combination of mass spectrometry, Raman microspectroscopy, circular dichroism and X-ray crystallography has been used to obtain detailed information on the reaction of an iridium-based CO-releasing molecule (Ir-CORM), Cs2IrCl5CO, with a model protein, bovine pancreatic ribonuclease. The results show that Ir-compound fragments bind to the N-terminal amine and close to histidine and methionine side chains, and the CO ligand is retained for a long time. The data provide helpful information for identifying protein targets for Ir-CORMs and for studying the mechanism that allows them to exhibit their interesting biological properties.

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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. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.64 kDa 
• Atom Count: 2,237 
• 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, B	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IR	C [auth A], F [auth A], H [auth A], J [auth A], K [auth B]	IRIDIUM ION Ir MOHYGSBMXIJZBJ-UHFFFAOYSA-N
CL	D [auth A], I [auth A], L [auth B], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO	E [auth A], G [auth A], M [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.932	α = 90
b = 32.652	β = 90.28
c = 72.273	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Caterino, M., Petruk, A.A., Vergara, A., Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-08-03
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description