Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.61 kDa 
• Atom Count: 495 
• Modelled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

1FXD

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

• PDB DOI: 10.2210/pdb1FXD/pdb

• Classification: ELECTRON TRANSFER(IRON-SULFUR)
• Organism(s): Desulfovibrio gigas
• Mutation(s): No 


• Deposited: 1991-04-08 Released: 1993-04-15 
• Deposition Author(s): Kissinger, C.R., Sieker, L.C., Adman, E.T., Jensen, L.H.

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Experimental Data Snapshot

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

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: 2056535 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERREDOXIN II	A	58	Desulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for P00209 (Megalodesulfovibrio gigas) Explore P00209  Go to UniProtKB:  P00209

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3S	B [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

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 = 40.87	α = 90
b = 45.28	β = 104.7
c = 26.47	γ = 90

Software Package:

Software Name	Purpose
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1991-04-08 
• Released Date: 1993-04-15 
Deposition Author(s): Kissinger, C.R., Sieker, L.C., Adman, E.T., Jensen, L.H.

Revision History  

• 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