3S0R | pdb_00003s0r

Crystal Structure of De novo Designed helical assembly protein

• PDB DOI: https://doi.org/10.2210/pdb3S0R/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2011-05-13 Released: 2011-06-15 
• Deposition Author(s): Acharya, R., Grigoryan, G., Kim, Y.H., DeGrado, W.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.275 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: in silico

Literature

Computational design of virus-like protein assemblies on carbon nanotube surfaces.

Grigoryan, G., Kim, Y.H., Acharya, R., Axelrod, K., Jain, R.M., Willis, L., Drndic, M., Kikkawa, J.M., DeGrado, W.F.

(2011) Science 332: 1071-1076

• PubMed: 21617073 
• DOI: https://doi.org/10.1126/science.1198841
• Primary Citation Related Structures: 
  3S0R


• PubMed Abstract: 
  

  There is a general need for the engineering of protein-like molecules that organize into geometrically specific superstructures on molecular surfaces, directing further functionalization to create richly textured, multilayered assemblies. Here we describe a computational approach whereby the surface properties and symmetry of a targeted surface define the sequence and superstructure of surface-organizing peptides. Computational design proceeds in a series of steps that encode both surface recognition and favorable intersubunit packing interactions. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes (SWNTs). The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of SWNTs into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the SWNT axis.

---

Organizational Affiliation: 
• Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.38 kDa 
• Atom Count: 464 
• Modeled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed Helical Assembly	A, B	30	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.275 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.529	α = 90
b = 45.529	β = 90
c = 93.293	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Acharya, R., Grigoryan, G., Kim, Y.H., DeGrado, W.F.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-17
  Changes: Source and taxonomy
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description