7ARR | pdb_00007arr

The de novo designed hybrid alpha/beta-miniprotein

• PDB DOI: https://doi.org/10.2210/pdb7ARR/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: 1.10 Å
• R-Value Free: 
  0.161 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

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 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.
Department of Bioorganic Chemistry Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland. [e-mail].
Department of Medical Biochemistry, Wrocław Medical University, Pausteura 1, Wroclaw 50-368, Poland.
Faculty of Chemistry, Jagiellonian Univeristy, Gronostajowa 2, Kraków 30-387, 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)

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: 16.55 kDa 
• Atom Count: 1,584 
• Modeled Residue Count: 136 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	E [auth A]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
CL	I [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], G [auth B], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.161 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Diffraction Data: https://doi.org/10.18150/EM87YL

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.937	α = 114.16
b = 32.068	β = 91.88
c = 43.087	γ = 109.86

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