7AX2 | pdb_00007ax2

Crystal structure of the computationally designed Scone-E protein co-crystallized with STA, form b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.206 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 45.69 kDa 
  • Atom Count: 2,534 
  • Modeled Residue Count: 311 
  • Deposited Residue Count: 358 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Scone-E358synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.206 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.517α = 90
b = 133.517β = 90
c = 70.093γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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 2.0: 2021-06-30
    Changes: Database references, Non-polymer description
  • Version 2.1: 2021-07-14
    Changes: Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description