9XZP | pdb_00009xzp

Crystal structure of AI-designed homodimer MIYEI

• PDB DOI: https://doi.org/10.2210/pdb9XZP/pdb

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


• Deposited: 2025-08-27 Released: 2025-10-22 
• Deposition Author(s): Wei, K.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.245 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.198 (DCC) 

Starting Model: in silico

Literature

An Artificial Intelligence Model for Translating Natural Language into Functional de Novo Proteins

Riley, T.P., Parsa, M.S., Kalantari, P., Naderi, I., Azimian, K., Begloo, N., Matusovsky, O., Azimian, K., Wei, K.Y.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.03.21.644400

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: 16.06 kDa 
• Atom Count: 1,298 
• Modeled Residue Count: 155 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo protein	A, B	78	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.245 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.198 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.093	α = 90
b = 53.473	β = 112.443
c = 55.786	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
Aimless	data scaling
TRUNCATE	data processing
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Wei, K.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Database references