5ON9

Crystal structure of NikA in complex with reduced Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions.

Lopez, S.Rondot, L.Lepretre, C.Marchi-Delapierre, C.Menage, S.Cavazza, C.

(2017) J Am Chem Soc 139: 17994-18002

  • DOI: https://doi.org/10.1021/jacs.7b09343
  • Primary Citation of Related Structures:  
    5ON0, 5ON1, 5ON4, 5ON5, 5ON8, 5ON9

  • PubMed Abstract: 

    Designing systems that merge the advantages of heterogeneous catalysis, enzymology, and molecular catalysis represents the next major goal for sustainable chemistry. Cross-linked enzyme crystals display most of these essential assets (well-designed mesoporous support, protein selectivity, and molecular recognition of substrates). Nevertheless, a lack of reaction diversity, particularly in the field of oxidation, remains a constraint for their increased use in the field. Here, thanks to the design of cross-linked artificial nonheme iron oxygenase crystals, we filled this gap by developing biobased heterogeneous catalysts capable of oxidizing carbon-carbon double bonds. First, reductive O 2 activation induces selective oxidative cleavage, revealing the indestructible character of the solid catalyst (at least 30 000 turnover numbers without any loss of activity). Second, the use of 2-electron oxidants allows selective and high-efficiency hydroxychlorination with thousands of turnover numbers. This new technology by far outperforms catalysis using the inorganic complexes alone, or even the artificial enzymes in solution. The combination of easy catalyst synthesis, the improvement of "omic" technologies, and automation of protein crystallization makes this strategy a real opportunity for the future of (bio)catalysis.


  • Organizational Affiliation

    Université Grenoble-Alpes , Grenoble F-38000, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9YH
Query on 9YH

Download Ideal Coordinates CCD File 
D [auth A],
P [auth B]
2-[2-[2-hydroxy-2-oxoethyl-[(3-methoxy-2-oxidanyl-phenyl)methyl]amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid
C22 H28 N2 O6 S
WFZIZUYYKZMMKQ-UHFFFAOYSA-N
DTT
Query on DTT

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
F [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A],
N [auth A],
T [auth B],
U [auth B],
V [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
O [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.9α = 90
b = 94.1β = 90
c = 124.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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-14-CE06-0005-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2020-08-19
    Changes: Derived calculations
  • Version 1.4: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description