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)

Macromolecule Content

• Total Structure Weight: 112.66 kDa 
• Atom Count: 8,755 
• Modelled Residue Count: 996 
• Deposited Residue Count: 1,000 
• Unique protein chains: 1

 4OER

Crystal structure of NikA from Brucella suis, unliganded form

• PDB DOI: 10.2210/pdb4OER/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Brucella suis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-13 Released: 2014-10-01 
• Deposition Author(s): Lebrette, H., Cavazza, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins.

Lebrette, H., Brochier-Armanet, C., Zambelli, B., de Reuse, H., Borezee-Durant, E., Ciurli, S., Cavazza, C.

(2014) Structure 22: 1421-1432

• PubMed: 25199691 
• DOI: 10.1016/j.str.2014.07.012
• Primary Citation of Related Structures:  
  4OER, 4OES, 4OET, 4OEU, 4OEV, 4OFL, 4OFO


• PubMed Abstract: 
  

In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.

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Organizational Affiliation: 

University Grenoble Alpes, LCBM, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NikA protein	A, B	500	Brucella suis	Mutation(s): 0  Gene Names: nikA, E4658_07960
UniProt
Find proteins for Q9AL82 (Brucella suis) Explore Q9AL82  Go to UniProtKB:  Q9AL82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth A], L [auth A], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.02	α = 90
b = 62.231	β = 105.3
c = 114.483	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Lebrette, H., Cavazza, C.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references