5L8D | pdb_00005l8d

X-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate scorpionate)(CO)2Cl

PDB DOI: https://doi.org/10.2210/pdb5L8D/pdb

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

Deposited: 2016-06-07 Released: 2017-03-29
Deposition Author(s): Menage, S., Cavazza, C.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.208 (Depositor), 0.195 (DCC)
R-Value Work:
0.168 (Depositor), 0.179 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Efficient conversion of alkenes to chlorohydrins by a Ru-based artificial enzyme.

Lopez, S., Rondot, L., Cavazza, C., Iannello, M., Boeri-Erba, E., Burzlaff, N., Strinitz, F., Jorge-Robin, A., Marchi-Delapierre, C., Menage, S.

(2017) Chem Commun (Camb) 53: 3579-3582

PubMed: 28289745 Search on PubMed
DOI: https://doi.org/10.1039/c6cc08873b
Primary Citation Related Structures:
5L8D

PubMed Abstract:
Artificial enzymes are required to catalyse non-natural reactions. Here, a hybrid catalyst was developed by embedding a novel Ru complex in the transport protein NikA. The protein scaffold activates the bound Ru complex to produce a catalyst with high regio- and stereo-selectivity. The hybrid efficiently and stably produced α-hydroxy-β-chloro chlorohydrins from alkenes (up to 180 TON with a TOF of 1050 h ^-1).

Organizational Affiliation

Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, BioCE, F-Grenoble, France and CNRS, Laboratoire de Chimie et Biologie des Métaux, BioCat, UMR 5249, France and CEA-Grenoble, DRF/BIG/CBM, F-Grenoble, France. stephane.menage@cea.fr.

Macromolecule Content

Total Structure Weight: 115.28 kDa
Atom Count: 8,824
Modeled Residue Count: 996
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDT Query on EDT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
6RP Query on 6RP Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	bis(pyrzol-1-yl)acetate scorpionate C₈ H₈ N₄ O₂ NJDSSVBTTVUKHM-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
RU Query on RU Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [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 U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain BA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [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 U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [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 U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain BA [auth B]	BA [auth B] G [auth A] GA [auth B] H [auth A] I [auth A] BA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain FA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain S [auth A] SDF format, chain T [auth B] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth B] MOL2 format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth B] mmCIF format, chain X [auth B]	C [auth A] D [auth A] E [auth A] FA [auth B] L [auth A] C [auth A], D [auth A], E [auth A], FA [auth B], L [auth A], M [auth A], N [auth A], S [auth A], T [auth B], X [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain FA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth A] Focus chain T [auth B] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain FA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth A] Focus chain T [auth B] Focus chain X [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain Z [auth B]	CA [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain Z [auth B]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B]	DA [auth B], EA [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.208 (Depositor), 0.195 (DCC)
R-Value Work: 0.168 (Depositor), 0.179 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.303	α = 90
b = 93.606	β = 90
c = 124.211	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Menage, S.

Cavazza, C.

Funding Organization	Location	Grant Number
French National Research Agency	France	14-CE06-0005-01

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2017-04-05
Changes: Atomic model, Database references
Version 1.2: 2017-08-30
Changes: Author supporting evidence
Version 1.3: 2019-06-12
Changes: Data collection, Structure summary
Version 1.4: 2019-10-16
Changes: Data collection
Version 1.5: 2024-01-10
Changes: Data collection, Database references, Refinement description