1FXD

REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.

Kissinger, C.R.Sieker, L.C.Adman, E.T.Jensen, L.H.

(1991) J.Mol.Biol. 219: 693-715


  • PubMed Abstract: 
  • The crystal structure of ferredoxin II from Desulfovibrio gigas has been determined using phasing from anomalous scattering data at a resolution of 1.7 A and refined to an R-factor of 0.157. The molecule has an overall chain fold similar to that of t ...

    The crystal structure of ferredoxin II from Desulfovibrio gigas has been determined using phasing from anomalous scattering data at a resolution of 1.7 A and refined to an R-factor of 0.157. The molecule has an overall chain fold similar to that of the other bacterial ferredoxins of known structure. The molecule contains a single 3Fe-4S cluster with geometry indistinguishable from the 4Fe-4S clusters, and a disulfide bond near the site corresponding to the position of the second cluster of two-cluster ferredoxins. The cluster is bound by cysteine residues 8, 14 and 50. The side-chain of cysteine 11 extends away from the cluster, but could rotate to become the fourth cysteine ligand in the four-iron form of the molecule given a local adjustment of the polypeptide chain. This residue is modified, however, by what appears to be a methanethiol group. There are a total of eight NH . . . S bonds to the inorganic and cysteine sulfur atoms of the Fe-S cluster. There is an additional residue found that is not reported for the chemical sequence: according to the electron density a valine residue should be inserted after residue 55.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Study of the 3-Fe Ferredoxin II from the Bacterium Desulfovibrio Gigas
      Sieker, L.C.,Adman, E.T.,Jensen, L.H.,Legall, J.
      (1984) J.Mol.Biol. 179: 151
    • The Crystal Structure of the Three-Iron Ferredoxin II from Desulfovibrio Gigas
      Kissinger, C.R.,Adman, E.T.,Sieker, L.C.,Jensen, L.H.,Legall, J.
      (1989) FEBS Lett. 244: 447
    • Structure of the 3Fe-4S Cluster in Desulfovibrio Gigas Ferredoxin II
      Kissinger, C.R.,Adman, E.T.,Sieker, L.C.,Jensen, L.H.
      (1988) J.Am.Chem.Soc. 110: 8721


    Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle 98195.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN II
A
58Desulfovibrio gigasN/A
Find proteins for P00209 (Desulfovibrio gigas)
Go to UniProtKB:  P00209
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download SDF File 
Download CCD File 
A
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
A
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 40.870α = 90.00
b = 45.280β = 104.70
c = 26.470γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other