2A3M

Structure of Desulfovibrio desulfuricans G20 tetraheme cytochrome (oxidized form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Desulfovibrio desulfuricans G20 Tetraheme Cytochrome Structure at 1.5A and Cytochrome Interaction with Metal Complexes

Pattarkine, M.V.Tanner, J.J.Bottoms, C.A.Lee, Y.H.Wall, J.D.

(2006) J.Mol.Biol. 358: 1314-1327

  • DOI: 10.1016/j.jmb.2006.03.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the type I tetraheme cytochrome c(3) from Desulfovibrio desulfuricans G20 was determined to 1.5 Angstrom by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determi ...

    The structure of the type I tetraheme cytochrome c(3) from Desulfovibrio desulfuricans G20 was determined to 1.5 Angstrom by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determined from oxidized crystals soaked in sodium molybdate. Only small structural shifts were obtained with metal binding, consistent with the remarkable structural stability of this protein. In vitro experiments with pure cytochrome showed that molybdate could oxidize the reduced cytochrome, although not as rapidly as U(VI) present as uranyl acetate. Alterations in the overall conformation and thermostability of the metal-oxidized protein were investigated by circular dichroism studies. Again, only small changes in protein structure were documented. The location of the molybdate ion near heme IV in the crystal structure suggested heme IV as the site of electron exit from the reduced cytochrome and implicated Lys14 and Lys56 in binding. Analysis of structurally conserved water molecules in type I cytochrome c(3) crystal structures identified interactions predicted to be important for protein stability and possibly for intramolecular electron transfer among heme molecules.


    Organizational Affiliation

    Biochemistry Department, University of Missouri-Columbia, Columbia, MO 65211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COG3005: Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit
A
130Desulfovibrio alaskensis (strain G20)Mutation(s): 0 
Find proteins for Q30WH0 (Desulfovibrio alaskensis (strain G20))
Go to UniProtKB:  Q30WH0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.670α = 90.00
b = 43.876β = 90.00
c = 57.729γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description