Crystal structures and thermostability of mutant TRAP3 A5 (ENGINEERED TRAP)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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Intersubunit linker length as a modifier of protein stability: crystal structures and thermostability of mutant TRAP.

Watanabe, M.Mishima, Y.Yamashita, I.Park, S.Y.Tame, J.R.Heddle, J.G.

(2008) Protein Sci 17: 518-526

  • DOI: https://doi.org/10.1110/ps.073059308
  • Primary Citation of Related Structures:  
    2ZCZ, 2ZD0

  • PubMed Abstract: 

    The ability of proteins to self-assemble into complex, functional nanoscale structures is expected to become of significant use in the manufacture of artificial nanodevices with a wide range of novel applications. The bacterial protein TRAP has potential uses as a nanoscale component as it is ring-shaped, with a central, modifiable cavity. Furthermore, it can be engineered to make a ring of 12-fold symmetry, which is advantageous for packing into two-dimensional arrays. The 12mer form of TRAP is made by linking multiple subunits together on the same polypeptide, but the usefulness of the 12mers described to date is limited by their poor stability. Here we show that, by altering the length of the peptide linker between subunits, the thermostability can be significantly improved. Since the subunit interfaces of the different 12mers are essentially identical, stabilization arises from the reduction of strain in the linkers. Such a simple method of controlling the stability of modular proteins may have wide applications, and demonstrates the lack of absolute correlation between interactions observable by crystallography and the internal energy of a complex.

  • Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription attenuation protein mtrB
A, B, C
79Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mtrB
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Explore Q9X6J6 
Go to UniProtKB:  Q9X6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6J6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.676α = 90
b = 109.676β = 90
c = 36.756γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-02-08
    Changes: Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description