8JU8 | pdb_00008ju8

de novo designed protein

• PDB DOI: https://doi.org/10.2210/pdb8JU8/pdb

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


• Deposited: 2023-06-25 Released: 2023-07-26 
• Deposition Author(s): Zhang, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

de novo designed Rossmann fold protein

Zhang, L.

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: 15.21 kDa 
• Atom Count: 1,234 
• Modeled Residue Count: 139 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
de novo designed protein	A	139	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.964	α = 90
b = 58.964	β = 90
c = 97.589	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Zhang, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection