5B6Q

Crystal structure of monomeric cytochrome c5 from Shewanella violacea

• PDB DOI: https://doi.org/10.2210/pdb5B6Q/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Shewanella violacea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2016-10-19 
• Deposition Author(s): Masanari, M., Fujii, S., Kawahara, K., Oki, H., Tsujino, H., Maruno, T., Kobayashi, Y., Ohkubo, T., Nishiyama, M., Harada, Y., Wakai, S., Sambongi, Y.

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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 

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 

• PubMed: 27648635 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.33 kDa 
• Atom Count: 1,361 
• Modelled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome cA	A, B	76	Shewanella violacea	Mutation(s): 0  Gene Names: cytcA
UniProt
Find proteins for D4ZE39 (Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)) Explore D4ZE39  Go to UniProtKB:  D4ZE39

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A], D [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
IMD	E [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

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 = 26.588	α = 90
b = 50.075	β = 90
c = 97.609	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Masanari, M., Fujii, S., Kawahara, K., Oki, H., Tsujino, H., Maruno, T., Kobayashi, Y., Ohkubo, T., Nishiyama, M., Harada, Y., Wakai, S., Sambongi, Y.

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