7OEC

Crystal structure of an intein from a hyperthermophile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins.

Hiltunen, M.K.Beyer, H.M.Iwai, H.

(2021) Microorganisms 9

  • DOI: https://doi.org/10.3390/microorganisms9061226
  • Primary Citation of Related Structures:  
    7OEC

  • PubMed Abstract: 

    Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few serve as widely used tools in protein engineering. We determined the crystal structure of a naturally occurring Pol-II mini-intein from Pyrococcus horikoshii and compared all three mini-inteins found in the genome of P. horikoshii . Despite their similar sizes, the comparison revealed distinct differences in the insertions and deletions, implying specific evolutionary pathways from distinct ancestral origins. Our studies suggest that sporadically distributed mini-inteins might be more promising for further protein engineering applications than highly conserved mini-inteins. Structural investigations of additional inteins could guide the shortest path to finding novel robust mini-inteins suitable for various protein engineering purposes.


  • Organizational Affiliation

    Institute of Biotechnology, HiLiFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase II large subunit169Pyrococcus horikoshii OT3Mutation(s): 2 
Gene Names: polCPH0121
EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (PDB Primary Data)
UniProt
Find proteins for O57861 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57861 
Go to UniProtKB:  O57861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57861
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.82α = 90
b = 70.82β = 90
c = 70.66γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
GDAdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland137995, 277335, 336450

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2021-08-18
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-31
    Changes: Refinement description