Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 115.87 kDa 
• Atom Count: 8,820 
• Modelled Residue Count: 994 
• Deposited Residue Count: 1,002 
• Unique protein chains: 1

 3MZB

X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2

• PDB DOI: 10.2210/pdb3MZB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-12 Released: 2011-02-09 
• Deposition Author(s): Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Crystallographic snapshots of the reaction of aromatic C-H with O(2) catalysed by a protein-bound iron complex

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

• PubMed: 21107372 
• DOI: 10.1038/nchem.841
• Primary Citation of Related Structures:  
  3MVW, 3MVX, 3MVY, 3MVZ, 3MW0, 3MZ9, 3MZB


• PubMed Abstract: 
  

Chemical reactions inside single crystals are quite rare because crystallinity is difficult to retain owing to atomic rearrangements. Protein crystals in general have a high solvent content. This allows for some molecular flexibility, which makes it possible to trap reaction intermediates of enzymatic reactions without disrupting the crystal lattice. A similar approach has not yet been fully implemented in the field of inorganic chemistry. Here, we have combined model chemistry and protein X-ray crystallography to study the intramolecular aromatic dihydroxylation by an arene-containing protein-bound iron complex. The bound complex was able to activate dioxygen in the presence of a reductant, leading to the formation of catechol as the sole product. The structure determination of four of the catalytic cycle intermediates and the end product showed that the hydroxylation reaction implicates an iron peroxo, generated by reductive O(2) activation, an intermediate already observed in iron monooxygenases. This strategy also provided unexpected mechanistic details such as the rearrangement of the iron coordination sphere on metal reduction.

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Organizational Affiliation: 

Laboratoire de Cristallographie et de Cristallogenèse des Protéines, Institut de Biologie Structurale J.P. Ebel, UMR 5075 CEA, CNRS, Université Joseph Fourier, 41 rue Horowitz, 38027 Grenoble Cedex 1, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B	501	Escherichia coli K-12	Mutation(s): 0  Gene Names: nikA, b3476, JW3441 EC: 3.6.3.24
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590  Go to UniProtKB:  P33590

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BHR	FA [auth B], U [auth A]	2-[2-[carboxymethyl-[(2-hydroxyphenyl)methyl]amino]ethyl-[(2,3-dihydroxyphenyl)methyl]amino]ethanoic acid C20 H24 N2 O7 PIRBWSIWJQHRSO-UHFFFAOYSA-N
DTD	HA [auth B], W [auth A]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
SO4	J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth A], DA [auth B], IA [auth B], JA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], Y [auth A], Z [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	BA [auth B], C [auth A], CA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], KA [auth B], LA [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	GA [auth B], V [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	EA [auth B], R [auth A], S [auth A], T [auth A], X [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.04	α = 90
b = 93.873	β = 90
c = 124.726	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance