3MVY | pdb_00003mvy

X-ray structure of the diatomic oxo-intermediate NikA/1-Int', prior hydroxylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3MVY

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/nchem.841
  • Primary Citation 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.


  • 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. christine.cavazza@ibs.fr

Macromolecule Content 

  • Total Structure Weight: 114.96 kDa 
  • Atom Count: 8,373 
  • Modeled Residue Count: 995 
  • Deposited Residue Count: 1,004 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nickel-binding periplasmic protein
A, B
502Escherichia coli K-12Mutation(s): 0 
Gene Names: nikA
EC: 3.6.3.24
UniProt
Find proteins for P33590 (Escherichia coli (strain K12))
Explore P33590 
Go to UniProtKB:  P33590
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33590
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BHZ

Query on BHZ



Download:Ideal Coordinates CCD File
K [auth A],
W [auth B]
2-[2-[carboxymethyl(phenylmethyl)amino]ethyl-[(2-hydroxyphenyl)methyl]amino]ethanoic acid
C20 H24 N2 O5
JSDNXVMPVNBNSK-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
O [auth A]
P [auth A]
G [auth A],
H [auth A],
I [auth A],
O [auth A],
P [auth A],
R [auth A],
U [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
Q [auth A]
S [auth B]
C [auth A],
D [auth A],
E [auth A],
Q [auth A],
S [auth B],
T [auth B],
Y [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE

Query on FE



Download:Ideal Coordinates CCD File
J [auth A],
V [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
PER

Query on PER



Download:Ideal Coordinates CCD File
L [auth A],
X [auth B]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.985α = 90
b = 95.172β = 90
c = 125.049γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description