7TJL | pdb_00007tjl

Crystal structure of de novo designed protein, SEWN0.1

• PDB DOI: https://doi.org/10.2210/pdb7TJL/pdb

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


• Deposited: 2022-01-16 Released: 2022-06-29 
• Deposition Author(s): Cummins, M.C., Jacobs, T.M., Kuhlman, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.231 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: in silico

Literature

AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein

Cummins, M.C., Jacobs, T.M., Teets, F.D., DiMaio, F., Tripathy, A., Kuhlman, B.

(2022) Protein Sci 31: 1-7

• DOI: https://doi.org/10.1002/pro.4368

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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 11.25 kDa 
• Atom Count: 825 
• Modeled Residue Count: 85 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed protein, SEWN0.1	A	93	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.231 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.25	α = 90
b = 31	β = 93.071
c = 31.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
SHELXE	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Cummins, M.C., Jacobs, T.M., Kuhlman, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM131923

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection
• Version 1.2: 2024-04-03
  Changes: Refinement description