3SNV

Crystal structure of Symfoil-4T Permutation #1: de novo designed beta-trefoil architecture with symmetric primary structure

• PDB DOI: https://doi.org/10.2210/pdb3SNV/pdb

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


• Deposited: 2011-06-29 Released: 2012-07-04 
• Deposition Author(s): Blaber, M., Longo, L., Lee, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.257 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Folding pathway redundancy in symmetric protein architecture

Longo, L., Lee, J., Blaber, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33 kDa 
• Atom Count: 2,061 
• Modelled Residue Count: 249 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Symfoil-4T/Permutation #1 synthetic protein	A, B	143	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.257 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.667	α = 90
b = 56.667	β = 90
c = 81.102	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Blaber, M., Longo, L., Lee, J.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description