4XKR | pdb_00004xkr

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

• PDB DOI: https://doi.org/10.2210/pdb4XKR/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Staphylococcus aureus USA300-ISMMS1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-12 Released: 2015-02-11 
• Deposition Author(s): Lebrette, H., Cavazza, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

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

• PubMed: 25611161 
• DOI: https://doi.org/10.1039/c4mt00295d
• Primary Citation 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.

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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 55.87 kDa 
• Atom Count: 4,436 
• Modeled Residue Count: 464 
• Deposited Residue Count: 473 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel ABC transporter substrate-binding protein	A	473	Staphylococcus aureus USA300-ISMMS1	Mutation(s): 0  Gene Names: AZ30_01190
UniProt
Find proteins for Q2G2P5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G2P5  Go to UniProtKB:  Q2G2P5

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
41K	D [auth A]	(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid C6 H9 N O4 S JCAKCGQZNBEITC-BBIVZNJYSA-N
HIS	C [auth A]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
NA	X [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.803	α = 90
b = 67.373	β = 90
c = 115.566	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Lebrette, H., Cavazza, C.

Revision History  

• 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