9MH2

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Adenosine and glycine complex)

• PDB DOI: https://doi.org/10.2210/pdb9MH2/pdb

• Classification: TRANSFERASE
• Organism(s): Trichomonas vaginalis G3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-11 Released: 2024-12-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.168 
• R-Value Work: 0.142 
• R-Value Observed: 0.143 

Starting Model: in silico

Literature

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Adenosine and glycine complex)

Seibold, S., Liu, L., Lovell, S., Battaile, K.P.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 27.1 kDa 
• Atom Count: 2,089 
• Modelled Residue Count: 239 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase, putative	A	244	Trichomonas vaginalis G3	Mutation(s): 0  Gene Names: TVAG_454490
UniProt
Find proteins for A2EU62 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2EU62  Go to UniProtKB:  A2EU62

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN (Subject of Investigation/LOI)	E [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
GLY	B [auth A], C [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.168 
• R-Value Work: 0.142 
• R-Value Observed: 0.143 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.033	α = 90
b = 93.033	β = 90
c = 130.449	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release