5F75 | pdb_00005f75

Thiocyanate dehydrogenase from Thioalkalivibrio paradoxus

• PDB DOI: https://doi.org/10.2210/pdb5F75/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thioalkalivibrio paradoxus
• Mutation(s): No 


• Deposited: 2015-12-07 Released: 2016-12-14 
• Deposition Author(s): Tsallagov, S.I., Polyakov, K.M., Tikhonova, T.V., Trofimov, A.A., Shabalin, I.G., Popov, A.N., Popov, V.O.
• Funding Organization(s): RFBR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Thiocyanate dehydrogenase from Thioalkalivibrio paradoxus

Tsallagov, S.I., Polyakov, K.M., Tikhonova, T.V., Trofimov, A.A., Shabalin, I.G., Popov, A.N., Popov, V.O.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 240.46 kDa 
• Atom Count: 15,038 
• Modeled Residue Count: 1,881 
• Deposited Residue Count: 2,192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocyanate dehydrogenase	A, B, C, D	548	Thioalkalivibrio paradoxus	Mutation(s): 0
UniProt
Find proteins for W0DP94 (Thioalkalivibrio paradoxus ARh 1) Explore W0DP94  Go to UniProtKB:  W0DP94

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.78	α = 90
b = 95.42	β = 100.66
c = 107	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Tsallagov, S.I., Polyakov, K.M., Tikhonova, T.V., Trofimov, A.A., Shabalin, I.G., Popov, A.N., Popov, V.O.

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Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-31304 mol_a

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description