9EXZ

Efficient and scalable protein design using a relaxed sequence space

• PDB DOI: https://doi.org/10.2210/pdb9EXZ/pdb

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


• Deposited: 2024-04-09 Released: 2024-10-16 
• Deposition Author(s): Frank, C.J., Dietz, H.
• Funding Organization(s): European Research Council (ERC), Germanys Excellence Strategy

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.279 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Starting Model: in silico

Literature

Efficient and scalable protein design using a relaxed sequence space

Frank, C.J., Dietz, H.

(2024) Science 

• DOI: https://doi.org/10.1126/science.adq1741

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 202.44 kDa 
• Atom Count: 13,929 
• Modelled Residue Count: 1,791 
• Deposited Residue Count: 1,827 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DE NOVO PROTEIN P600	A, B, C	609	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.279 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.249	α = 90
b = 67.825	β = 103.2
c = 173.693	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Frank, C.J., Dietz, H.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	GA101018465
Germanys Excellence Strategy	Germany	TUM Innovation Network Projekt RISE

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release