8SPM

Crystal structure of NikA in complex Ni-AMA

• PDB DOI: https://doi.org/10.2210/pdb8SPM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-03 Released: 2024-04-10 
• Deposition Author(s): Sychantha, D., Prehna, G., Wright, G.D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.242 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Targeting bacterial nickel transport inhibits virulence-associated Ni-dependent enzymes

Sychantha, D., Koteva, K., Prehna, G., Wright, G.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.43 kDa 
• Atom Count: 4,078 
• Modelled Residue Count: 499 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel ABC transporter, nickel/metallophore periplasmic binding protein	A	499	Escherichia coli	Mutation(s): 0  Gene Names: nikA
UniProt
Find proteins for A0A024L032 (Escherichia coli) Explore A0A024L032  Go to UniProtKB:  A0A024L032

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
II1 (Subject of Investigation/LOI)	B [auth A]	Aspergillomarasmine A C10 H17 N3 O8 XFTWUNOVBCHBJR-ZLUOBGJFSA-N
NI (Subject of Investigation/LOI)	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.242 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.42	α = 90
b = 66.42	β = 90
c = 267.77	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Sychantha, D., Prehna, G., Wright, G.D.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FRN-148463
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2018-04968

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release