6R4Q | pdb_00006r4q

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl

PDB DOI: https://doi.org/10.2210/pdb6R4Q/pdb

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

Deposited: 2019-03-22 Released: 2020-04-08
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:
0.232 (Depositor), 0.239 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl

Cavazza, C., Menage, S.

To be published.

Macromolecule Content

Total Structure Weight: 115.68 kDa
Atom Count: 8,848
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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDT Query on EDT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
6RP Query on 6RP Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	bis(pyrzol-1-yl)acetate scorpionate C₈ H₈ N₄ O₂ NJDSSVBTTVUKHM-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
RU Query on RU Download:Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], P [auth A], Q [auth A], S [auth A], U [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain U [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain U [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain N [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain N [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain N [auth A]	GA [auth B] HA [auth B] M [auth A] N [auth A] O [auth A] GA [auth B], HA [auth B], M [auth A], N [auth A], O [auth A], R [auth A], T [auth A], V [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth A] Focus chain T [auth A] Focus chain V [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth A] Focus chain T [auth A] Focus chain V [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Y [auth B] MOL2 format, chain E [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain E [auth A] mmCIF format, chain Y [auth B]	E [auth A], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain Y [auth B] Interactions & Density Focus chain E [auth A] Focus chain Y [auth B]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232 (Depositor), 0.239 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.629	α = 90
b = 94.101	β = 90
c = 124.418	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Cavazza, C.

Menage, S.

Funding Organization	Location	Grant Number
French National Research Agency	France	Crystalball

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description