1QJD

Flavocytochrome C3 from Shewanella frigidimarina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Mechanistic Mapping of a Unique Fumarate Reductase

Taylor, P.Pealing, S.L.Reid, G.A.Chapman, S.K.Walkinshaw, M.D.

(1999) Nat Struct Biol 6: 1108

  • DOI: https://doi.org/10.1038/70045
  • Primary Citation of Related Structures:  
    1QJD

  • PubMed Abstract: 

    The 1.8 A resolution crystal structure of the tetraheme flavocytochrome c3, Fcc3, provides the first mechanistic insight into respiratory fumarate reductases or succinate dehydrogenases. The multi-redox center, three-domain protein shows a 40 A long 'molecular wire' allowing rapid conduction of electrons through a new type of cytochrome domain onto the active site flavin, driving the reduction of fumarate to succinate. In this structure a malate-like molecule is trapped in the enzyme active site. The interactions between this molecule and the enzyme suggest a clear mechanism for fumarate reduction in which the substrate is polarized and twisted, facilitating hydride transfer from the reduced flavin and subsequent proton transfer. The enzyme active site in the oxidized form is completely buried at the interface between the flavin-binding and the clamp domains. Movement of the cytochrome and clamp domains is postulated to allow release of the product.


  • Organizational Affiliation

    Institute of Cell and Molecular Biology, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FLAVOCYTOCHROME C3571Shewanella frigidimarinaMutation(s): 0 
UniProt
Find proteins for Q07WU7 (Shewanella frigidimarina (strain NCIMB 400))
Explore Q07WU7 
Go to UniProtKB:  Q07WU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07WU7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
TEO
Query on TEO

Download Ideal Coordinates CCD File 
G [auth A]MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.393α = 90
b = 91.946β = 91.09
c = 78.288γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
SOLVEphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-21
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2019-05-22
    Changes: Data collection, Refinement description