7AWY

Crystal structure of the computationally designed Scone-R protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of Scone: pseudosymmetric folding of a symmetric designer protein.

Mylemans, B.Killian, T.Vandebroek, L.Van Meervelt, L.Tame, J.R.H.Parac-Vogt, T.N.Voet, A.R.D.

(2021) Acta Crystallogr D Struct Biol 77: 933-942

  • DOI: https://doi.org/10.1107/S2059798321005787
  • Primary Citation of Related Structures:  
    7AWY, 7AWZ, 7AX0, 7AX2

  • PubMed Abstract: 

    Recent years have seen an increase in the development of computational proteins, including symmetric ones. A ninefold-symmetric β-propeller protein named Cake has recently been developed. Here, attempts were made to further engineer this protein into a threefold-symmetric nine-bladed propeller using computational design. Two nine-bladed propeller proteins were designed, named Scone-E and Scone-R. Crystallography, however, revealed the structure of both designs to adopt an eightfold conformation with distorted termini, leading to a pseudo-symmetric protein. One of the proteins could only be crystallized upon the addition of a polyoxometalate, highlighting the usefulness of these molecules as crystallization additives.


  • Organizational Affiliation

    Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Vlaams Brabant, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Scone-R358synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.077α = 90
b = 79.834β = 100.984
c = 47.426γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumGBM-D3229-ASP/17
Research Foundation - Flanders (FWO)BelgiumG0E4717N
Research Foundation - Flanders (FWO)BelgiumG051917N
Research Foundation - Flanders (FWO)BelgiumG0F9316N

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description