1DFX | pdb_00001dfx

DESULFOFERRODOXIN FROM DESULFOVIBRIO DESULFURICANS, ATCC 27774

• PDB DOI: https://doi.org/10.2210/pdb1DFX/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Desulfovibrio desulfuricans
• Mutation(s): No 


• Deposited: 1997-09-03 Released: 1998-10-14 
• Deposition Author(s): Coelho, A.V., Matias, P.M., Carrondo, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Desulfoferrodoxin Structure Determined by MAD Phasing and Refinement to 1.9 Angstroms Resolution Reveals a Unique Combination of a Tetrahedral Fes4 Centre with a Square Pyramidal Fesn4 Centre

Coelho, A.V., Matias, P., Fulop, V., Thompson, A., Gonzalez, A., Carrondo, M.A.

(1997) J Biol Inorg Chem 2: 680

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 14.06 kDa 
• Atom Count: 1,048 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DESULFOFERRODOXIN	A	125	Desulfovibrio desulfuricans	Mutation(s): 0  EC: 1.15.1.2
UniProt
Find proteins for P22076 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore P22076  Go to UniProtKB:  P22076

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.5	α = 90
b = 112.5	β = 90
c = 63.2	γ = 120

Software Package:

Software Name	Purpose
SHELXL-93	model building
SHELXL-93	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXL-93	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Coelho, A.V., Matias, P.M., Carrondo, M.A.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other