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), 0.140 (DCC) 
• R-Value Work: 
  0.114 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.116 (Depositor) 

Literature

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

Varfolomeeva, L.A., Solovieva, A.Y., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

To be published.

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 
• Modelled 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), 0.140 (DCC) 
• R-Value Work:  0.114 (Depositor), 0.110 (DCC) 
• 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