5B6Q

Crystal structure of monomeric cytochrome c5 from Shewanella violacea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Literature

Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea

Masanari, M.Fujii, S.Kawahara, K.Oki, H.Tsujino, H.Maruno, T.Kobayashi, Y.Ohkubo, T.Wakai, S.Sambongi, Y.

(2016) Biosci Biotechnol Biochem 

  • DOI: 10.1080/09168451.2016.1232155
  • Primary Citation of Related Structures:  
    5B6Q

  • PubMed Abstract: 
  • Monomeric cytochrome c 5 from deep-sea piezophilic Shewanella violacea (SVcytc 5 ) was stable against heat and denaturant compared with the homologous protein from shallow-sea piezo-sensitive Shewanella livingstonensis (SLcytc

    Monomeric cytochrome c 5 from deep-sea piezophilic Shewanella violacea (SVcytc 5 ) was stable against heat and denaturant compared with the homologous protein from shallow-sea piezo-sensitive Shewanella livingstonensis (SLcytc 5 ). Here, the SVcytc 5 crystal structure revealed that the Lys-50 side chain on the flexible loop formed a hydrogen bond with heme whereas that of corresponding hydrophobic Leu-50 could not form such a bond in SLcytc 5 , which appeared to be one of possible factors responsible for the difference in stability between the two proteins. This structural insight was confirmed by a reciprocal mutagenesis study on the thermal stability of these two proteins. As SVcytc 5 was isolated from a deep-sea piezophilic bacterium, the present comparative study indicates that adaptation of monomeric SVcytc 5 to high pressure environments results in stabilization against heat.


    Organizational Affiliation

    a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome cA AB76Shewanella violaceaMutation(s): 0 
Gene Names: cytcA
Find proteins for D4ZE39 (Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12))
Explore D4ZE39 
Go to UniProtKB:  D4ZE39
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.588α = 90
b = 50.075β = 90
c = 97.609γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary