5VJS | pdb_00005vjs

De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, a synthetic Zn porphyrin, and Zn(II) cations

• PDB DOI: https://doi.org/10.2210/pdb5VJS/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-19 Released: 2018-04-25 
• Deposition Author(s): Ennist, N.M., Dutton, P.L., Stayrook, S.E., Moser, C.C.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

De novo protein design of photochemical reaction centers.

Ennist, N.M., Zhao, Z., Stayrook, S.E., Discher, B.M., Dutton, P.L., Moser, C.C.

(2022) Nat Commun 13: 4937-4937

• PubMed: 35999239 
• DOI: https://doi.org/10.1038/s41467-022-32710-5
• Primary Citation Related Structures: 
  5VJS, 5VJT, 5VJU


• PubMed Abstract: 
  

  Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here, we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. [e-mail].
Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA.
Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA.
Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT, 06516, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.95 kDa 
• Atom Count: 1,729 
• Modeled Residue Count: 196 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction Center Maquette	A	196	synthetic construct	Mutation(s): 0  Gene Names: designed

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
9D7	C [auth A]	[4-(15-phenylporphyrin-5-yl-kappa~4~N~21~,N~22~,N~23~,N~24~)benzoato(2-)]zinc C33 H20 N4 O2 Zn BQOXGOKXDBIPTM-LTTHWXANSA-M
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.749	α = 90
b = 43.749	β = 90
c = 245.737	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Ennist, N.M., Dutton, P.L., Stayrook, S.E., Moser, C.C.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DESC0001035

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Author supporting evidence, Data collection, Database references
• Version 1.2: 2022-08-31
  Changes: Database references
• Version 1.3: 2024-05-22
  Changes: Data collection