1SJ1 | pdb_00001sj1

The 1.5 A Resolution Crystal Structure of [Fe3S4]-Ferredoxin from the hyperthermophilic Archaeon Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb1SJ1/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-02 Released: 2004-05-25 
• Deposition Author(s): Nielsen, M.S., Harris, P., Ooi, B.L., Christensen, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.223 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

The 1.5 A Resolution Crystal Structure of [Fe3S4]-Ferredoxin from the Hyperthermophilic Archaeon Pyrococcus furiosus

Nielsen, M.S., Harris, P., Ooi, B.L., Christensen, H.E.M.

(2004) Biochemistry 43: 5188-5194

• PubMed: 15122884 
• DOI: https://doi.org/10.1021/bi049942x
• Primary Citation Related Structures: 
  1SIZ, 1SJ1


• PubMed Abstract: 
  

  The structure of [Fe(3)S(4)]-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus has been determined to 1.5 A resolution from a crystal belonging to space group P2(1) with two molecules in the asymmetric unit. The structure has been solved with molecular replacement by use of the ferredoxin from Thermotoga maritima. The fold is similar to that of related monocluster ferredoxins and contains two double-stranded antiparallel beta-sheets and two alpha-helices. The hydrophobic interaction between Trp2 and Tyr46 is confirmed, linking the C-terminus to the longer alpha-helix. The structure contains a double-conformation disulfide bond existing in a left-handed and a right-handed spiral conformation. The crystal packing reveals a beta-sheet interaction, which supports the suggestion that P. furiosus ferredoxin is a functional dimer. The extraordinary thermostability of P. furiosus ferredoxin is further discussed.

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Organizational Affiliation: 
• Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.58 kDa 
• Atom Count: 1,305 
• Modeled Residue Count: 132 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A, B	66	Pyrococcus furiosus	Mutation(s): 0  Gene Names: FDXA, PF1909
UniProt
Find proteins for P29603 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P29603  Go to UniProtKB:  P29603

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3S	E [auth A], H [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
NCO	C [auth A], D [auth A], F [auth B], G [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.223 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.23	α = 90
b = 47.511	β = 103.86
c = 52.029	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Nielsen, M.S., Harris, P., Ooi, B.L., Christensen, H.E.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary