2JI2

X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form

• PDB DOI: https://doi.org/10.2210/pdb2JI2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfarculus baarsii
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2007-02-24 Released: 2007-05-01 
• Deposition Author(s): Katona, G., Carpentier, P., Niviere, V., Amara, P., Adam, V., Ohana, J., Tsanov, N., Bourgeois, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.222 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.

Katona, G., Carpentier, P., Niviere, V., Amara, P., Adam, V., Ohana, J., Tsanov, N., Bourgeois, D.

(2007) Science 316: 449-453

• PubMed: 17446401 
• DOI: https://doi.org/10.1126/science.1138885
• Primary Citation of Related Structures:  
  2JI1, 2JI2, 2JI3


• PubMed Abstract: 
  

  Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.

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Organizational Affiliation: 

Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France.

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 PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 57.33 kDa 
• Atom Count: 4,534 
• Modelled Residue Count: 502 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Desulfoferrodoxin	A, B, C, D	126	Desulfarculus baarsii	Mutation(s): 1  Gene Names: dfx, rbo, Deba_2050 EC: 1.15.1.2
UniProt
Find proteins for Q46495 (Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14)) Explore Q46495  Go to UniProtKB:  Q46495

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	F [auth A], I [auth B], M [auth C], S [auth D]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
FE2	G [auth A], K [auth B], Q [auth C], T [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
FE	E [auth A], H [auth B], L [auth C], R [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	J [auth B], N [auth C], O [auth C], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.222 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.47	α = 90
b = 82.87	β = 90
c = 201.95	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Katona, G., Carpentier, P., Niviere, V., Amara, P., Adam, V., Ohana, J., Tsanov, N., Bourgeois, D.

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2018-06-27
  Changes: Data collection, Derived calculations
• Version 1.5: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.6: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description