1KQF

FORMATE DEHYDROGENASE N FROM E. COLI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.

Jormakka, M., Tornroth, S., Byrne, B., Iwata, S.

(2002) Science 295: 1863-1868

  • DOI: 10.1126/science.1068186
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinuc ...

    The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.

    Organizational Affiliation: 

    Division of Biomedical Sciences, Imperial College, London SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
A
1015Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fdnG
EC: 1.17.5.3
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Formate dehydrogenase-N
Find proteins for P24183 (Escherichia coli (strain K12))
Go to UniProtKB:  P24183
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
B
294Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fdnH
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Formate dehydrogenase-N
Find proteins for P0AAJ3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AAJ3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT
C
217Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fdnI
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Formate dehydrogenase-N
Find proteins for P0AEK7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEK7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CDL
Query on CDL
Download SDF File 
Download CCD File 
C
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
6MO
Query on 6MO
Download SDF File 
Download CCD File 
A
MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD
Download SDF File 
Download CCD File 
A
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 203.000α = 90.00
b = 203.000β = 90.00
c = 203.000γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2014-02-19
    Type: Atomic model, Structure summary
  • Version 1.4: 2014-08-06
    Type: Derived calculations, Structure summary