7UNI

De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM

• PDB DOI: https://doi.org/10.2210/pdb7UNI/pdb

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


• Deposited: 2022-04-11 Released: 2023-04-19 
• Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Ennist, N.M.
• Funding Organization(s): National Science Foundation (NSF, United States), Advanced Research Projects Agency-Energy (ARPA-E), Audacious Project at the Institute for Protein Design

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.252 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM

Kennedy, M.A., Stoddard, B.L., Ennist, N.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 112.27 kDa 
• Atom Count: 6,899 
• Modelled Residue Count: 968 
• Deposited Residue Count: 1,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SP2-ZnPPaM designed chlorophyll dimer protein	A, B [auth C], C [auth B], D	250	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OE9 (Subject of Investigation/LOI)	E [auth A], I [auth C], L [auth B], N [auth D]	[methyl 9-ethenyl-14-ethyl-3-(3-methoxy-3-oxopropyl)-4,8,13,18-tetramethyl-20-oxophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc C36 H36 N4 O5 Zn KSFOOHVZTTVNHW-PIFGRXHESA-M
PGE	H [auth A], M [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	F [auth A], J [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	G [auth A], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.252 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.855	α = 87.83
b = 54.961	β = 84.06
c = 89.365	γ = 69.45

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Ennist, N.M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-1762114
Advanced Research Projects Agency-Energy (ARPA-E)		DE-AR0001543
Audacious Project at the Institute for Protein Design		68-2492: Audacious GC5: Next-Generation Nanoengineering

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description