8YTS | pdb_00008yts

The structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb8YTS/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thioalkalivibrio paradoxus ARh 1
• Mutation(s): No 


• Deposited: 2024-03-26 Released: 2024-04-24 
• Deposition Author(s): Varfolomeeva, L.A., Solovieva, A.Y., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.144 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.114 (Depositor) 
• R-Value Observed: 
  0.116 (Depositor) 

Literature

Relationship between the structure and physicochemical properties of cytochrome c 546/556 from the bacterium Thioalkalivibrio paradoxus ARh1.

Varfolomeeva, L.A., Solovieva, A.Y., Shipkov, N.S., Sluchanko, N.N., Boyko, K.M., Khrenova, M.G., Tikhonova, T.V., Popov, V.O.

(2025) Biochem Biophys Res Commun 778: 152340-152340

• PubMed: 40669334 
• DOI: https://doi.org/10.1016/j.bbrc.2025.152340
• Primary Citation Related Structures: 
  8YTS


• PubMed Abstract: 
  

  An interplay between the structural and physicochemical properties of the monoheme cytochromes of type c has been extensively studied. However new proteins belonging to this diverse family continue to reveal some novel and unique features. Here, we present the 1.15 Å structure of the low-potential cytochrome c _546/556 from the bacterium Thioalkalivibrio paradoxus ARh1, which exhibits the prominent splitting of the Q bands in UV-visible spectra even at room temperature. The data obtained suggest that two conformations of the propionate 7 of the heme are responsible for the splitting of the Q bands. We propose that the degree of the splitting of the Q bands is correlated with the conformational lability of the heme propionates.

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Organizational Affiliation: 
• Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow, 119071, Russian Federation. Electronic address: [e-mail].
Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow, 119071, Russian Federation.
Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow, 119071, Russian Federation; Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation.
Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow, 119071, Russian Federation; Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow, 119991, Russian Federation.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.29 kDa 
• Atom Count: 1,580 
• Modeled Residue Count: 166 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome C	A, B	105	Thioalkalivibrio paradoxus ARh 1	Mutation(s): 0
UniProt
Find proteins for W0DLP1 (Thioalkalivibrio paradoxus ARh 1) Explore W0DLP1  Go to UniProtKB:  W0DLP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	C [auth A], D [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.144 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.114 (Depositor) 
• R-Value Observed: 0.116 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.416	α = 90
b = 37.601	β = 90
c = 97.117	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CRANK2	phasing
DIALS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Varfolomeeva, L.A., Solovieva, A.Y., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-07-23
  Changes: Database references
• Version 1.3: 2025-07-30
  Changes: Database references