9L6D | pdb_00009l6d

the crystal structure of Azurin-LBT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Literature

Engineering a Hetero-Bimetallic Azurin Photoenzyme for Photoredox Nitrite Reduction and SNO Adduct Formation.

Su, B.Yu, Y.Liu, H.Li, C.

(2025) Chemistry 31: e202500143-e202500143

  • DOI: https://doi.org/10.1002/chem.202500143
  • Primary Citation of Related Structures:  
    9L6D

  • PubMed Abstract: 

    Photoredox catalysis in protein systems presents exciting opportunities to achieve sustainable and efficient enzymatic reactions driven by light. Here, we report the design and characterization of PhotoNiR, an engineered azurin-based protein incorporating a red copper center and a lanthanide-binding tag (LBT). This dual-metal system enables photoredox reduction of nitrite to nitric oxide via a proposed donor-f-electron-acceptor (D-f-A) electron transfer mechanism. Upon photoirradiation, aromatic residues in the LBT donate electrons to the lanthanide ion, which relays them to the Cu(II) center, reducing it to Cu(I). The reduced Cu(I)-PhotoNiR catalyzes the reduction of NO 2 - , and the generated NO subsequently reacts with free cysteine residues to form S-nitrosothiol (SNO) species. Spectroscopic and structural characterization confirmed that the copper center retains the properties of a red copper site and that the lanthanide-binding tag supports efficient electron transfer. This work represents one of the first examples of a D-f-A mechanism in a protein system, demonstrating the potential of integrating metalloprotein engineering with lanthanide photochemistry to develop novel photoenzymes for light-driven catalysis.


  • Organizational Affiliation
    • Department: Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Azurin
A, B, C
148Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: azuPA4922
UniProt
Find proteins for P00282 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P00282 
Go to UniProtKB:  P00282
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00282
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TB (Subject of Investigation/LOI)
Query on TB

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
L [auth C],
M [auth C]
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
K [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.855α = 90
b = 87.096β = 112.59
c = 78.823γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release