7A0C

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

PDB DOI: https://doi.org/10.2210/pdb7A0C/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-07 Released: 2020-11-04
Deposition Author(s): Cavazza, C., Menage, S.
Funding Organization(s): French National Research Agency

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 33079395 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 115.14 kDa
Atom Count: 8,957
Modelled Residue Count: 996
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B	502	Escherichia coli K-12	Mutation(s): 0 Gene Names: nikA, b3476, JW3441
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590 Go to UniProtKB: P33590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QTT Query on QTT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain T [auth B] MOL2 format, chain D [auth A] MOL2 format, chain T [auth B] mmCIF format, chain D [auth A] mmCIF format, chain T [auth B]	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		Interactions Focus chain D [auth A] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	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		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain U [auth B] mmCIF format, chain C [auth A] mmCIF format, chain U [auth B]	C [auth A], U [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain DA [auth B]	DA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Interactions & Density Focus chain DA [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain S [auth A] SDF format, chain Z [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B]	AA [auth B], BA [auth B], CA [auth B], S [auth A], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain S [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain S [auth A] Focus chain Z [auth B]

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 = 86.809	α = 90
b = 93.796	β = 90
c = 124.222	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-04

Deposition Author(s):

Cavazza, C.

Menage, S.

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-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