5N1T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
flavin-binding subunit of sulfide dehydrogenase
A
429Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Find proteins for W0DP88 (Thioalkalivibrio paradoxus ARh 1)
Go to UniProtKB:  W0DP88
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome C
B
102Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Find proteins for W0DKT4 (Thioalkalivibrio paradoxus ARh 1)
Go to UniProtKB:  W0DKT4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CopC
M, W
160Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Find proteins for W0DSL1 (Thioalkalivibrio paradoxus ARh 1)
Go to UniProtKB:  W0DSL1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
W
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
W
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-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: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.530α = 90.00
b = 138.400β = 90.00
c = 155.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RNFRussian Federation14-24-00172

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references