Hallucinated de novo TIM barrel with two helical extensions - HalluTIM2-2

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report

This is version 1.0 of the entry. See complete history


Diversifying de novo TIM barrels by hallucination.

Beck, J.Shanmugaratnam, S.Hocker, B.

(2024) Protein Sci 33: e5001-e5001

  • DOI: https://doi.org/10.1002/pro.5001
  • Primary Citation of Related Structures:  
    8R8N, 8R8O

  • PubMed Abstract: 

    De novo protein design expands the protein universe by creating new sequences to accomplish tailor-made enzymes in the future. A promising topology to implement diverse enzyme functions is the ubiquitous TIM-barrel fold. Since the initial de novo design of an idealized four-fold symmetric TIM barrel, the family of de novo TIM barrels is expanding rapidly. Despite this and in contrast to natural TIM barrels, these novel proteins lack cavities and structural elements essential for the incorporation of binding sites or enzymatic functions. In this work, we diversified a de novo TIM barrel by extending multiple βα-loops using constrained hallucination. Experimentally tested designs were found to be soluble upon expression in Escherichia coli and well-behaved. Biochemical characterization and crystal structures revealed successful extensions with defined α-helical structures. These diversified de novo TIM barrels provide a framework to explore a broad spectrum of functions based on the potential of natural TIM barrels.

  • Organizational Affiliation

    Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
251synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.71α = 90
b = 71.2β = 90
c = 88.64γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release