8OQG

Cross-linked crystal of dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (high temperature data collection)

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

  • Deposited: 2023-04-12 Released: 2023-06-14 
  • Deposition Author(s): Loreto, D., Merlino, A., Maity, B., Ueno, T.
  • Funding Organization(s): University of Naples Federico II, Compagnia di San Paolo Foundation, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.182 

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Literature

Cross-Linked Crystals of Dirhodium Tetraacetate/RNase A Adduct Can Be Used as Heterogeneous Catalysts.

Loreto, D.Maity, B.Morita, T.Nakamura, H.Merlino, A.Ueno, T.

(2023) Inorg Chem 62: 7515-7524

  • DOI: https://doi.org/10.1021/acs.inorgchem.3c00852
  • Primary Citation of Related Structures:  
    8OQC, 8OQD, 8OQE, 8OQF, 8OQG

  • PubMed Abstract: 

    Due to their unique coordination structure, dirhodium paddlewheel complexes are of interest in several research fields, like medicinal chemistry, catalysis, etc. Previously, these complexes were conjugated to proteins and peptides for developing artificial metalloenzymes as homogeneous catalysts. Fixation of dirhodium complexes into protein crystals is interesting to develop heterogeneous catalysts. Porous solvent channels present in protein crystals can benefit the activity by increasing the probability of substrate collisions at the catalytic Rh binding sites. Toward this goal, the present work describes the use of bovine pancreatic ribonuclease (RNase A) crystals with a pore size of 4 nm ( P 3 2 21 space group) for fixing [Rh 2 (OAc) 4 ] and developing a heterogeneous catalyst to perform reactions in an aqueous medium. The structure of the [Rh 2 (OAc) 4 ]/RNase A adduct was investigated by X-ray crystallography: the metal complex structure remains unperturbed upon protein binding. Using a number of crystal structures, metal complex accumulation over time, within the RNase A crystals, and structures at variable temperatures were evaluated. We also report the large-scale preparation of microcrystals (∼10-20 μm) of the [Rh 2 (OAc) 4 ]/RNase A adduct and cross-linking reaction with glutaraldehyde. The catalytic olefin cyclopropanation reaction and self-coupling of diazo compounds by these cross-linked [Rh 2 (OAc) 4 ]/RNase A crystals were demonstrated. The results of this work reveal that these systems can be used as heterogeneous catalysts to promote reactions in aqueous solution. Overall, our findings demonstrate that the dirhodium paddlewheel complexes can be fixed in porous biomolecule crystals, like those of RNase A, to prepare biohybrid materials for catalytic applications.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Napoli I-80126, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic124Bos taurusMutation(s): 0 
EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.278α = 90
b = 67.278β = 90
c = 65.899γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of Naples Federico IIItaly--
Compagnia di San Paolo FoundationItaly--
Japan Society for the Promotion of Science (JSPS)Japan22H00347
Japan Society for the Promotion of Science (JSPS)JapanJP18H05421

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release