8KC4

De novo design protein -NA05

• PDB DOI: https://doi.org/10.2210/pdb8KC4/pdb

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


• Deposited: 2023-08-06 Released: 2024-08-07 
• Deposition Author(s): Wang, S., Liu, Y.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: in silico

Literature

De novo design protein -NA05

Wang, S., Liu, Y.

To be published.

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: 18.56 kDa 
• Atom Count: 1,140 
• Modelled Residue Count: 151 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo design protein -NA05	A	162	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.535	α = 90
b = 59.101	β = 90
c = 67.956	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Wang, S., Liu, Y.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release