1A70 | pdb_00001a70

SPINACH FERREDOXIN

• PDB DOI: https://doi.org/10.2210/pdb1A70/pdb

• Classification: IRON-SULFUR PROTEIN
• Organism(s): Spinacia oleracea
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-03-19 Released: 1998-11-25 
• Deposition Author(s): Binda, C., Coda, A., Mattevi, A., Aliverti, A., Zanetti, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.200 (Depositor) 
• R-Value Work: 
  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution.

Binda, C., Coda, A., Aliverti, A., Zanetti, G., Mattevi, A.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1353-1358

• PubMed: 10089511 
• DOI: https://doi.org/10.1107/s0907444998005137
• Primary Citation Related Structures: 
  1A70


• PubMed Abstract: 
  

  Ferredoxin I (Fd I) from Spinacia oleracea is composed of 97 amino-acid residues and a [2Fe-2S] cluster. The crystal structure of the E92K mutant of Fd I was solved by molecular replacement and refined to an R factor of 19.6% for 11755 reflections at 1.7 A resolution. The overall structure and the active centre of spinach Fd is highly conserved with respect to ferredoxins of known structure. The E92K mutation appears to disturb a hydrogen-bond network which stabilizes the loop bearing the [2Fe-2S] cluster. This observation provides a rationale for the reduced electron-transfer efficiency displayed by the E92K mutant. Inspection of the crystal packing reveals that the side chain of Lys92 is engaged in an intermolecular interaction with Asp26 of a symmetry-related molecule. This feature may explain why only the mutant E92K and not wild-type Fd I could be successfully crystallized.

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Organizational Affiliation: 
• Dipartimento di Genetica e Microbiologia, Università di Pavia, via Abbiategrasso 207, 27100 Pavia, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.66 kDa 
• Atom Count: 817 
• Modeled Residue Count: 97 
• Deposited Residue Count: 97 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERREDOXIN	A	97	Spinacia oleracea	Mutation(s): 1
UniProt
Find proteins for P00221 (Spinacia oleracea) Explore P00221  Go to UniProtKB:  P00221

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.200 (Depositor) 
• R-Value Work:  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31	α = 90
b = 39.18	β = 90
c = 83.52	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
TNT	refinement
MOSFLM	data reduction
Agrovata	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-25 
Deposition Author(s): Binda, C., Coda, A., Mattevi, A., Aliverti, A., Zanetti, G.

Revision History  

• Version 1.0: 1998-11-25
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2023-08-02
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection