8SJG | pdb_00008sjg

Zn-Bound Structure of Computationally Designed Homotrimer Tet4

• PDB DOI: https://doi.org/10.2210/pdb8SJG/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-18 Released: 2023-07-05 
• Deposition Author(s): Hoffnagle, A.M., Tezcan, F.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.286 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries.

Hoffnagle, A.M., Tezcan, F.A.

(2023) J Am Chem Soc 145: 14208-14214

• PubMed: 37352018 
• DOI: https://doi.org/10.1021/jacs.3c04047
• Primary Citation Related Structures: 
  8SJF, 8SJG, 8SJH, 8SJI


• PubMed Abstract: 
  

  We report a new computational protein design method for the construction of oligomeric protein assemblies around metal centers with predefined coordination geometries. We apply this method to design two homotrimeric assemblies, Tet4 and TP1, with tetrahedral and trigonal-pyramidal tris(histidine) metal coordination geometries, respectively, and demonstrate that both assemblies form the targeted metal centers with ≤0.2 Å accuracy. Although Tet4 and TP1 are constructed from the same parent protein building block, they are distinct in terms of their overall architectures, the environment surrounding the metal centers, and their metal-based reactivities, illustrating the versatility of our approach.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 25.25 kDa 
• Atom Count: 1,657 
• Modeled Residue Count: 212 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tet4	A, B	114	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.286 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.663	α = 90
b = 67.663	β = 90
c = 109.635	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
APEX	data reduction
APEX	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Hoffnagle, A.M., Tezcan, F.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM138884

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-07-12
  Changes: Database references
• Version 1.2: 2024-05-22
  Changes: Data collection