5L8D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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

  • DOI: https://doi.org/10.1039/c6cc08873b
  • Primary Citation of 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. [email protected].


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 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDT
Query on EDT

Download Ideal Coordinates CCD File 
K [auth A]{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
6RP
Query on 6RP

Download Ideal Coordinates CCD File 
AA [auth B]bis(pyrzol-1-yl)acetate scorpionate
C8 H8 N4 O2
NJDSSVBTTVUKHM-UHFFFAOYSA-N
RU
Query on RU

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Y [auth B]RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
SO4
Query on SO4

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F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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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
ACT
Query on ACT

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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
FE
Query on FE

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J [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

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CA [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO
Query on CMO

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DA [auth B],
EA [auth B]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.303α = 90
b = 93.606β = 90
c = 124.211γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance14-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