4I8C | pdb_00004i8c

X-ray structure of NikA in complex with Ni-(L-His)2

PDB DOI: https://doi.org/10.2210/pdb4I8C/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-12-03 Released: 2013-01-30
Deposition Author(s): Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.234 (Depositor), 0.217 (DCC)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.191 (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

The binding mode of Ni-((L)-His)(2) in NikA revealed by X-ray crystallography.

Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

(2012) J Inorg Biochem 121C: 16-18

PubMed: 23314594 Search on PubMed
DOI: https://doi.org/10.1016/j.jinorgbio.2012.12.010
Primary Citation Related Structures:
4I8C

PubMed Abstract:
The ABC-type importer NikABCDE mediates nickel acquisition in Escherichia coli. The periplasmic nickel-binding component NikA has a folding similar to that of the peptide transporter OppA and does not bind free nickel. Instead, we showed that the metal is tetra-coordinated by an organic tri-dentate molecule and His416. Conversely, it has been recently reported that NikA binds Ni-(L-His)2 and that addition of histidine increases the rate of nickel uptake in vivo. Here, we report the structure of NikA/Ni-(L-His)2 and show that histidine binding differs from peptide binding in OppA. The structure also confirms the central role of His416 in nickel binding.

Organizational Affiliation

Institut de Biologie Structurale Jean-Pierre Ebel, Metalloproteins Group, UMR 5075, CEA, CNRS, Université Joseph Fourier-Grenoble 1, 41, rue Jules Horowitz 38027 Grenoble Cedex 1, France.

Macromolecule Content

Total Structure Weight: 172.1 kDa
Atom Count: 12,432
Modeled Residue Count: 1,494
Deposited Residue Count: 1,506
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, C	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIS Query on HIS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	D [auth A] E [auth A] EA [auth C] FA [auth C] Q [auth B] D [auth A], E [auth A], EA [auth C], FA [auth C], Q [auth B], R [auth B]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth B] Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain CA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain CA [auth B]	CA [auth B], MA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain MA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain MA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] KA [auth C] LA [auth C] N [auth A] AA [auth B], BA [auth B], KA [auth C], LA [auth C], N [auth A], O [auth A], P [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain M [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth B]	DA [auth B] G [auth A] H [auth A] HA [auth C] I [auth A] DA [auth B], G [auth A], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain DA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain GA [auth C] SDF format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain S [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain F [auth A]	F [auth A], GA [auth C], S [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth C] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain GA [auth C] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234 (Depositor), 0.217 (DCC)
R-Value Work: 0.189 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.63	α = 90
b = 158.63	β = 90
c = 135.82	γ = 120

Software Package:

Software Name	Purpose
MX	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-01-30

Deposition Author(s):

Lebrette, H.

Iannello, M.

Fontecilla-Camps, J.C.

Cavazza, C.

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description