6G50 | pdb_00006g50

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.207 (Depositor), 0.144 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6G50

This is version 1.3 of the entry. See complete history

Literature

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase.

Tikhonova, T.V.Sorokin, D.Y.Hagen, W.R.Khrenova, M.G.Muyzer, G.Rakitina, T.V.Shabalin, I.G.Trofimov, A.A.Tsallagov, S.I.Popov, V.O.

(2020) Proc Natl Acad Sci U S A 117: 5280-5290

  • DOI: https://doi.org/10.1073/pnas.1922133117
  • Primary Citation Related Structures: 
    6G50, 6I3Q, 6SJI, 6UWE

  • PubMed Abstract: 

    Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.


  • Organizational Affiliation
    • Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia.

Macromolecule Content 

  • Total Structure Weight: 208.69 kDa 
  • Atom Count: 16,327 
  • Modeled Residue Count: 1,868 
  • Deposited Residue Count: 1,868 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D
467Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
UniProt
Find proteins for W0DP94 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DP94 
Go to UniProtKB:  W0DP94
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DP94
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth D]
H [auth A]
M [auth B]
Q [auth C]
R [auth C]
AA [auth D],
H [auth A],
M [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
W [auth D],
X [auth D],
Y [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth D],
CA [auth D],
U [auth C],
V [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.207 (Depositor), 0.144 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.63α = 90
b = 162.28β = 119.51
c = 90.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian FederationGrant 14-24-00172

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Advisory, Data collection
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description