3KTX | pdb_00003ktx

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK)in complex with 1,3,6,8-pyrenetetrasulfonic acid

• PDB DOI: https://doi.org/10.2210/pdb3KTX/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-26 Released: 2010-02-09 
• Deposition Author(s): Morgan, H.P., Walkinshaw, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

An improved strategy for the crystallization of Leishmania mexicana pyruvate kinase.

Morgan, H.P., McNae, I.W., Hsin, K.Y., Michels, P.A., Fothergill-Gilmore, L.A., Walkinshaw, M.D.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 215-218

• PubMed: 20208146 
• DOI: https://doi.org/10.1107/S1744309109053494
• Primary Citation Related Structures: 
  3IS4, 3KTX


• PubMed Abstract: 
  

  The inclusion of novel small molecules in crystallization experiments has provided very encouraging results and this method is now emerging as a promising alternative strategy for crystallizing 'problematic' biological macromolecules. These small molecules have the ability to promote lattice formation through stabilizing intermolecular interactions in protein crystals. Here, the use of 1,3,6,8-pyrenetetrasulfonic acid (PTS), which provides a helpful intermolecular bridge between Leishmania mexicana PYK (LmPYK) macromolecules in the crystal, is reported, resulting in the rapid formation of a more stable crystal lattice at neutral pH and greatly improved X-ray diffraction results. The refined structure of the LmPYK-PTS complex revealed the negatively charged PTS molecule to be stacked between positively charged (surface-exposed) arginine side chains from neighbouring LmPYK molecules in the crystal lattice.

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Organizational Affiliation: 
• Structural Biochemistry Group, Institute of Structural and Molecular Biology, The University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 110.01 kDa 
• Atom Count: 8,214 
• Modeled Residue Count: 984 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B	499	Leishmania mexicana	Mutation(s): 0  Gene Names: PYK EC: 2.7.1.40
UniProt
Find proteins for Q27686 (Leishmania mexicana) Explore Q27686  Go to UniProtKB:  Q27686

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTK	E [auth A]	pyrene-1,3,6,8-tetrasulfonic acid C16 H10 O12 S4 CZLSHVQVNDDHDQ-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], F [auth A], G [auth A], H [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.86	α = 90
b = 129.86	β = 90
c = 165.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Morgan, H.P., Walkinshaw, M.D.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-28
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description