9MIT | pdb_00009mit

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Hepes bound)

PDB DOI: https://doi.org/10.2210/pdb9MIT/pdb

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

Deposited: 2024-12-13 Released: 2024-12-25
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.168 (Depositor), 0.175 (DCC)
R-Value Work:
0.147 (Depositor), 0.157 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Hepes bound)

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

To be published.

Macromolecule Content

Total Structure Weight: 160.89 kDa
Atom Count: 12,374
Modeled Residue Count: 1,418
Deposited Residue Count: 1,464
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase, putative	A, B, C, D, E A, B, C, D, E, F	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2EU62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D]	H [auth B], K [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain G [auth A]	G [auth A] I [auth B] J [auth C] L [auth D] M [auth E] G [auth A], I [auth B], J [auth C], L [auth D], M [auth E], N [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.168 (Depositor), 0.175 (DCC)
R-Value Work: 0.147 (Depositor), 0.157 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39MIT

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.816	α = 90
b = 49.713	β = 99.18
c = 175.122	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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