5MWU

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)(CO)2Cl

PDB DOI: https://doi.org/10.2210/pdb5MWU/pdb

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

Deposited: 2017-01-20 Released: 2017-02-22
Deposition Author(s): Cavazza, C., Lopez, S., Rondot, L., Iannello, M., Boeri-Erba, E., Burzlaff, N., Strinitz, F., Jorge-Robin, A., Marchi-Delapierre, C., Menage, S.
Funding Organization(s): French National Research Agency

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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, N., Jorge-Robin, A., Marchi-Delapierre, C., Menage, S.

To be published.

Macromolecule Content

Total Structure Weight: 115.28 kDa
Atom Count: 8,823
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 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]	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]	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]	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]	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 DA [auth B] SDF format, chain H [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain I [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] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain I [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]	DA [auth B] G [auth A] GA [auth B] H [auth A] I [auth A] DA [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 DA [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 DA [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 E [auth A] SDF format, chain N [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain FA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth A] SDF format, chain T [auth B] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth B] MOL2 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]	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 EA [auth B] SDF format, chain Z [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain Z [auth B]	EA [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth B] Focus chain Z [auth B] Interactions & Density Focus chain EA [auth B] Focus chain Z [auth B]
CMO Query on CMO Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B]	BA [auth B], CA [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B]

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 = 86.303	α = 90
b = 93.606	β = 90
c = 124.211	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Marchi-Delapierre, C.

Menage, S.

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

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2018-11-21
Changes: Data collection
Version 1.3: 2019-10-16
Changes: Data collection
Version 1.4: 2024-01-17
Changes: Data collection, Database references, Refinement description