4XKP

Crystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 (co-crystallization with Ni(II) and BHI medium supernatant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel insights into nickel import in Staphylococcus aureus: the positive role of free histidine and structural characterization of a new thiazolidine-type nickel chelator.

Lebrette, H.Borezee-Durant, E.Martin, L.Richaud, P.Boeri Erba, E.Cavazza, C.

(2015) Metallomics 7: 613-621

  • DOI: https://doi.org/10.1039/c4mt00295d
  • Primary Citation of Related Structures:  
    4OFJ, 4XKN, 4XKP, 4XKQ, 4XKR

  • PubMed Abstract: 

    Staphylococcus aureus possesses two canonical ABC-importers dedicated to nickel acquisition: the NikABCDE and the CntABCDF systems, active under different growth conditions. This study reports on the extracytoplasmic nickel-binding components SaNikA and SaCntA. We showed by protein crystallography that SaNikA is able to bind either a Ni-(l-His)2 complex or a Ni-(l-His) (2-methyl-thiazolidine dicarboxylate) complex, depending on their availability in culture supernatants. Native mass spectrometry experiments on SaCntA revealed that it binds the Ni(ii) ion via a different histidine-dependent chelator but it cannot bind Ni-(l-His)2. In vitro experiments are consistent with in vivo nickel content measurements that showed that l-histidine has a high positive impact on nickel import via the Cnt system. These results suggest that although both systems may require free histidine, they use different strategies to import nickel.


  • Organizational Affiliation

    Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nickel ABC transporter substrate-binding protein473Staphylococcus aureus USA300-ISMMS1Mutation(s): 0 
Gene Names: AZ30_01190
UniProt
Find proteins for Q2G2P5 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G2P5 
Go to UniProtKB:  Q2G2P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G2P5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
HIS
Query on HIS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth A]
I [auth A]
J [auth A]
E [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.34α = 90
b = 67.24β = 90
c = 115.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description