4I8C

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 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/j.jinorgbio.2012.12.010
• Primary Citation of 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 172.1 kDa 
• Atom Count: 12,432 
• Modelled Residue Count: 1,494 
• Deposited Residue Count: 1,506 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HIS	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
SO4	CA [auth B], MA [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	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
ACT	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
NI	F [auth A], GA [auth C], S [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• 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

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

Revision History  

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