5N1T

Crystal structure of complex between flavocytochrome c and copper chaperone CopC from T. paradoxus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Literature

Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1.

Osipov, E.M.Lilina, A.V.Tsallagov, S.I.Safonova, T.N.Sorokin, D.Y.Tikhonova, T.V.Popov, V.O.

(2018) Acta Crystallogr D Struct Biol 74: 632-642

  • DOI: https://doi.org/10.1107/S2059798318005648
  • Primary Citation of Related Structures:  
    5N1T

  • PubMed Abstract: 

    Flavocytochrome c sulfide dehydrogenase from Thioalkalivibrio paradoxus (TpFCC) is a heterodimeric protein consisting of flavin- and monohaem c-binding subunits. TpFCC was co-purified and co-crystallized with the dimeric copper-binding protein TpCopC. The structure of the TpFCC-(TpCopC) 2 complex was determined by X-ray diffraction at 2.6 Å resolution. The flavin-binding subunit of TpFCC is structurally similar to those determined previously, and the structure of the haem-binding subunit is similar to that of the N-terminal domain of dihaem FCCs. According to classification based on amino-acid sequence, TpCopC belongs to a high-affinity CopC subfamily characterized by the presence of a conserved His1-Xxx-His3 motif at the N-terminus. Apparently, a unique α-helix which is present in each monomer of TpCopC at the interface with TpFCC plays a key role in complex formation. The structure of the copper-binding site in TpCopC is similar to those in other known CopC structures. His3 is not involved in binding to the copper ion and is 6-7 Å away from this ion. Therefore, the His1-Xxx-His3 motif cannot be considered to be a key factor in the high affinity of CopC for copper(II) ions. It is suggested that the TpFCC-(TpCopC) 2 heterotetramer may be a component of a large periplasmic complex that is responsible for thiocyanate metabolism.


  • Organizational Affiliation

    Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Avenue, Building 2, Moscow 119071, Russian Federation.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
flavin-binding subunit of sulfide dehydrogenase429Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
UniProt
Find proteins for W0DP88 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DP88 
Go to UniProtKB:  W0DP88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DP88
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome C102Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
UniProt
Find proteins for W0DKT4 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DKT4 
Go to UniProtKB:  W0DKT4
Entity Groups  
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UniProt GroupW0DKT4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CopCC [auth M],
D [auth W]
160Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
UniProt
Find proteins for W0DSL1 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DSL1 
Go to UniProtKB:  W0DSL1
Entity Groups  
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UniProt GroupW0DSL1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.53α = 90
b = 138.4β = 90
c = 155.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RNFRussian Federation14-24-00172

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description