7A0C

X-ray structure of NikA from Escherichia coli in complex with Fe-6-Me2-BPMCN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A Selective Sulfide Oxidation Catalyzed by Heterogeneous Artificial Metalloenzymes Iron@NikA.

Lopez, S.Marchi-Delapierre, C.Cavazza, C.Menage, S.

(2020) Chemistry 26: 16633-16638

  • DOI: https://doi.org/10.1002/chem.202003746
  • Primary Citation of Related Structures:  
    7A0C

  • PubMed Abstract: 

    Performing a heterogeneous catalysis with proteins is still a challenge. Herein, we demonstrate the importance of cross-linked crystals for sulfoxide oxidation by an artificial enzyme. The biohybrid consists of the insertion of an iron complex into a NikA protein crystal. The heterogeneous catalysts displays a better efficiency-with higher reaction kinetics, a better stability and expand the substrate scope compared to its solution counterpart. Designing crystalline artificial enzymes represents a good alternative to soluble or supported enzymes for the future of synthetic biology.


  • Organizational Affiliation

    CEA, CNRS, IRIG, CBM, Univ. Grenoble Alpes, 38000, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nickel-binding periplasmic protein
A, B
502Escherichia coli K-12Mutation(s): 0 
Gene Names: nikAb3476JW3441
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
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QTT
Query on QTT

Download Ideal Coordinates CCD File 
D [auth A],
T [auth B]
2-[[(1~{S},2~{S})-2-[methyl-[(6-methylpyridin-2-yl)methyl]amino]cyclohexyl]-[(6-methylpyridin-2-yl)methyl]amino]ethanoic acid
C23 H32 N4 O2
SKWHQCFCFFYXHR-VXKWHMMOSA-N
GOL
Query on GOL

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N [auth A]
O [auth A]
P [auth A]
Q [auth A]
R [auth A]
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE
Query on FE

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C [auth A],
U [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

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DA [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AA [auth B],
BA [auth B],
CA [auth B],
S [auth A],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.809α = 90
b = 93.796β = 90
c = 124.222γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-18-CE07-0034-02

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-23
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description