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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
flavin-binding subunit of sulfide dehydrogenaseA429Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Gene Names: THITH_13285
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome CB102Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Gene Names: THITH_13280
UniProt
Find proteins for W0DKT4 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DKT4 
Go to UniProtKB:  W0DKT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DKT4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CopCC [auth M],
D [auth W]
160Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Gene Names: THITH_13340
UniProt
Find proteins for W0DSL1 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DSL1 
Go to UniProtKB:  W0DSL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DSL1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEC
Query on HEC

Download Ideal Coordinates CCD File 
F [auth B]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth W]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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G [auth W]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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