3EMV

Crystal structure of Plasmodium vivax PNP with sulphate

• PDB DOI: https://doi.org/10.2210/pdb3EMV/pdb

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


• Deposited: 2008-09-25 Released: 2009-08-04 
• Deposition Author(s): Chaikuad, A., Brady, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases

Chaikuad, A., Brady, R.L.

(2009) BMC Struct Biol 9: 42-42

• PubMed: 19575810 
• DOI: https://doi.org/10.1186/1472-6807-9-42
• Primary Citation of Related Structures:  
  3EMV, 3ENZ


• PubMed Abstract: 
  

  Purine nucleoside phosphorylase (PNP) is central to purine salvage mechanisms in Plasmodium parasites, the causative agents of malaria. Most human malaria results from infection either by Plasmodium falciparum (Pf), the deadliest form of the parasite, or by the widespread Plasmodium vivax (Pv). Whereas the PNP enzyme from Pf has previously been studied in detail, despite the prevalence of Pv little is known about many of the key metabolic enzymes from this parasite, including PvPNP.

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Organizational Affiliation: 

Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 28.42 kDa 
• Atom Count: 2,001 
• Modelled Residue Count: 246 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase, putative	A	253	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_080575 EC: 2.4.2.1
UniProt
Find proteins for A5K9M4 (Plasmodium vivax (strain Salvador I)) Explore A5K9M4  Go to UniProtKB:  A5K9M4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.749	α = 90
b = 94.749	β = 90
c = 121.254	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Chaikuad, A., Brady, R.L.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description