3SK3

Crystal structure of Salmonella typhimurium acetate kinase (AckA) with citrate bound at the dimeric interface

• PDB DOI: https://doi.org/10.2210/pdb3SK3/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-22 Released: 2012-08-29 
• Deposition Author(s): Chittori, S., Savithri, H.S., Murthy, M.R.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

Chittori, S., Savithri, H.S., Murthy, M.R.N.

(2012) BMC Struct Biol 12: 24-24

• PubMed: 23031654 
• DOI: https://doi.org/10.1186/1472-6807-12-24
• Primary Citation of Related Structures:  
  3SK3, 3SLC


• PubMed Abstract: 
  

  Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 90.55 kDa 
• Atom Count: 6,309 
• Modelled Residue Count: 772 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetate kinase	A, B	415	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: ackA EC: 2.7.2.1
UniProt
Find proteins for P63411 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P63411  Go to UniProtKB:  P63411

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.012	α = 90
b = 78.5	β = 116.37
c = 97.48	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Chittori, S., Savithri, H.S., Murthy, M.R.N.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description