6A3L

Crystal structure of cytochrome c' from Shewanella violacea DSS12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Stability of cytochromes c' from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure.

Suka, A.Oki, H.Kato, Y.Kawahara, K.Ohkubo, T.Maruno, T.Kobayashi, Y.Fujii, S.Wakai, S.Lisdiana, L.Sambongi, Y.

(2019) Extremophiles 23: 239-248

  • DOI: https://doi.org/10.1007/s00792-019-01077-9
  • Primary Citation of Related Structures:  
    6A3K, 6A3L

  • PubMed Abstract: 

    The stability of dimeric cytochrome c' from a thermophile, as compared with that of a homologous mesophilic counterpart, is attributed to strengthened interactions around the heme and at the subunit-subunit interface, both of which are molecular interior regions. Here, we showed that interactions in the equivalent interior regions of homologous cytochromes c' from two psychrophiles, Shewanella benthica and Shewanella violacea (SBCP and SVCP, respectively) were similarly weakened as compared with those of the counterparts of psychrophilic Shewanella livingstonensis and mesophilic Shewanella amazonensis (SLCP and SACP, respectively), and consistently the stability of SVCP, SLCP, and SACP increased in that order. Therefore, the stability of cytochromes c' from the psychrophile, mesophile, and thermophile is systematically regulated in their molecular interior regions. Unexpectedly, however, the stability of SBCP was significantly higher than that of SVCP, and the former had additional molecular surface interactions. Collectively, SBCP had weakened interior interactions like SVCP did, but the former was stabilized at the molecular surface as compared with the latter, implying complex multiple adaptation of the proteins because the psychrophilic sources of SBCP and SVCP are also piezophilic, thriving in deep-sea extreme environments of low temperature and high hydrostatic pressure.


  • Organizational Affiliation

    Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 1-4-4 Kagamiyama, Hiroshima, 739-8528, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
A, B
129Shewanella violacea DSS12Mutation(s): 0 
Gene Names: SVI_0970
UniProt
Find proteins for D4ZGZ2 (Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12))
Explore D4ZGZ2 
Go to UniProtKB:  D4ZGZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4ZGZ2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.751α = 90
b = 69.707β = 112.19
c = 45.598γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
CrystalCleardata collection
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary