1FXD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.157 

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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

  • DOI: 10.1016/0022-2836(91)90665-s
  • Primary Citation of Related Structures:  
    1FXD

  • 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 the other bacterial ferredoxins of known structure ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERREDOXIN IIA58Desulfovibrio gigasMutation(s): 0 
UniProt
Find proteins for P00209 (Megalodesulfovibrio gigas)
Explore P00209 
Go to UniProtKB:  P00209
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00209
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download Ideal Coordinates CCD File 
B [auth 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: 1.70 Å
  • R-Value Observed: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.87α = 90
b = 45.28β = 104.7
c = 26.47γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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