7YLK

Myoglobin containing Ir complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Photocatalytic C-O Coupling Enzymes That Operate via Intramolecular Electron Transfer.

Lee, J.Song, W.J.

(2023) J Am Chem Soc 145: 5211-5221

  • DOI: https://doi.org/10.1021/jacs.2c12226
  • Primary Citation of Related Structures:  
    7YLK

  • PubMed Abstract: 

    Efficient and environmentally friendly conversion of light energy for direct utilization in chemical production has been a long-standing goal in enzyme design. Herein, we synthesized artificial photocatalytic enzymes by introducing an Ir photocatalyst and a Ni(bpy) complex to an optimal protein scaffold in close proximity. Consequently, the enzyme generated C-O coupling products with up to 96% yields by harvesting visible light and performing intramolecular electron transfer between the two catalysts. We systematically modulated the catalytic activities of the artificial photocatalytic cross-coupling enzymes by tuning the electrochemical properties of the catalytic components, their positions, and distances within a protein. As a result, we discovered the best-performing mutant that showed broad substrate scopes under optimized conditions. This work explicitly demonstrated that we could integrate and control both the inorganic and biochemical components of photocatalytic biocatalysis to achieve high yield and selectivity in valuable chemical transformations.


  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin153Physeter catodonMutation(s): 5 
Gene Names: MB
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IRQ
Query on IRQ

Download Ideal Coordinates CCD File 
C [auth A]lambda-{1-([2,2'-bipyridin]-5-ylmethyl)pyrrolidine-2,5-dione}bis[2-(2,4-difluorophenyl)pyridine)]iridium(III)
C37 H25 F4 Ir N5 O2
QUFXSILAYVLQGU-UHFFFAOYSA-N
KKC
Query on KKC

Download Ideal Coordinates CCD File 
B [auth A]delta-{1-([2,2'-bipyridin]-5-ylmethyl)pyrrolidine-2,5-dione}bis[2-(2,4-difluorophenyl)pyridine)]iridium(III)
C37 H25 F4 Ir N5 O2
QUFXSILAYVLQGU-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BP5
Query on BP5
A
L-PEPTIDE LINKINGC13 H13 N3 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.402α = 90
b = 57.882β = 90
c = 76.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
Cootmodel building
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-11-29
    Changes: Refinement description