8TM9 | pdb_00008tm9

Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x bound to peptide

• PDB DOI: https://doi.org/10.2210/pdb8TM9/pdb

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


• Deposited: 2023-07-28 Released: 2024-12-11 
• Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Hicks, D.R.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: in silico

Literature

Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x bound to peptide

Kennedy, M.A., Stoddard, B.L., Hicks, D.R.

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

Macromolecule Content 

• Total Structure Weight: 55.55 kDa 
• Atom Count: 3,633 
• Modeled Residue Count: 461 
• Deposited Residue Count: 476 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D_3_633_8x peptide bound	A, B	234	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MC1	C [auth D]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
POL	D [auth A], H [auth B], I [auth B]	N-PROPANOL C3 H8 O BDERNNFJNOPAEC-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	C [auth D]	D-PEPTIDE LINKING	C3 H7 N O2		--
DPR	C [auth D]	D-PEPTIDE LINKING	C5 H9 N O2		--
MEA	C [auth D]	L-PEPTIDE LINKING	C10 H13 N O2		PHE
MLE	C [auth D]	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.717	α = 90
b = 54.562	β = 96.11
c = 80.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Hicks, D.R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-1762114
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM139752
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	R01AG063845
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	U19AG065156

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release