7ARS

The de novo designed hybrid alpha/beta-miniprotein (with Se-Methionine)

• PDB DOI: https://doi.org/10.2210/pdb7ARS/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2020-10-26 Released: 2021-07-14 
• Deposition Author(s): Bejger, M., Fortuna, P., Drewniak-Switalska, M., Rypniewski, W., Berlicki, L.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.220 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Starting Model: other

Literature

A computationally designed beta-amino acid-containing miniprotein.

Bejger, M., Fortuna, P., Drewniak-Switalska, M., Plewka, J., Rypniewski, W., Berlicki, L.

(2021) Chem Commun (Camb) 57: 6015-6018

• PubMed: 34032224 
• DOI: https://doi.org/10.1039/d1cc02192c
• Primary Citation of Related Structures:  
  7ARR, 7ARS


• PubMed Abstract: 
  

  A new miniprotein built from three helices, including one structure based on the ααβαααβ sequence pattern was developed. Its crystal structure revealed a compact conformation with a well-packed hydrophobic core of unprecedented structure. The miniprotein formed dimers that were stabilized by the interaction of their hydrophobic surfaces.

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Organizational Affiliation: 

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland.

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)

Macromolecule Content

• Total Structure Weight: 8.43 kDa 
• Atom Count: 835 
• Modelled Residue Count: 62 
• Deposited Residue Count: 70 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha/beta-peptide	A, B	35	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	C [auth A]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.220 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18150/CJTRKZ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.089	α = 90
b = 35.481	β = 111.24
c = 41.919	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Bejger, M., Fortuna, P., Drewniak-Switalska, M., Rypniewski, W., Berlicki, L.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	DEC-2016/21/B/ST5/00269

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description