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 (Depositor), 0.190 (DCC)
R-Value Work:
0.168 (Depositor), 0.180 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

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

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(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] 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 DA [auth B] 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 G [auth A] MOL2 format, chain DA [auth B] 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 G [auth A] mmCIF format, chain DA [auth B] 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 G [auth A]	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 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] SDF 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] MOL2 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] mmCIF format, chain C [auth A]	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 EA [auth B] SDF format, chain Z [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain EA [auth B] mmCIF 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] mmCIF format, chain BA [auth B] mmCIF 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 (Depositor), 0.190 (DCC)
R-Value Work: 0.168 (Depositor), 0.180 (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
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