2Z8Q | pdb_00002z8q

ferredoxin from Pyrococcus furiosus, D14C variant

• PDB DOI: https://doi.org/10.2210/pdb2Z8Q/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-09-07 Released: 2007-09-18 
• Deposition Author(s): Johannessen, M.N., Christensen, H.E.M., Harris, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the all cysteinyl coordinated D14C variant of [4Fe-4S] Pyrococcus furiosus ferredoxin

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.67 kDa 
• Atom Count: 1,248 
• 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 DSM 3638	Mutation(s): 1  Gene Names: fdxA
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
SF4	C [auth A], F [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
NCO	D [auth A], E [auth A], G [auth B], H [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 116.8	β = 90
c = 47.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Johannessen, M.N., Christensen, H.E.M., Harris, P.

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-23
  Changes: Atomic model
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary