1QJD

Flavocytochrome C3 from Shewanella frigidimarina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.267 

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.Mol.Biol. 6: 1108

  • DOI: 10.1038/70045

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FLAVOCYTOCHROME C3
A
571Shewanella frigidimarina (strain NCIMB 400)Mutation(s): 0 
Gene Names: fccA (fcc3)
EC: 1.3.5.4
Find proteins for Q07WU7 (Shewanella frigidimarina (strain NCIMB 400))
Go to UniProtKB:  Q07WU7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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

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

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Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
TEO
Query on TEO

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Download CCD File 
A
MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.267 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.393α = 90.00
b = 91.946β = 91.09
c = 78.288γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
DENZOdata reduction
SOLVEphasing
SHELXL-97phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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