9R2K | pdb_00009r2k

De novo designed N30 protein fold

• PDB DOI: https://doi.org/10.2210/pdb9R2K/pdb

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


• Deposited: 2025-04-30 Released: 2025-05-14 
• Deposition Author(s): Pacesa, M., Miao, Y., Georgeon, S., Schmidt, J., Correia, B.E.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Leveraging protein representations to explore uncharted fold spaces with generative models

Miao, Y., Pacesa, M., Georgeon, S., Schmidt, J., Lu, T., Huang, P.S., Correia, B.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.10.10.681606

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.66 kDa 
• Atom Count: 1,573 
• Modeled Residue Count: 177 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N30	A	189	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.6	α = 90
b = 39.81	β = 99.35
c = 54.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Pacesa, M., Miao, Y., Georgeon, S., Schmidt, J., Correia, B.E.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-11-26
  Changes: Database references