4GIE | pdb_00004gie

Crystal structure of prostaglandin F synthase from Trypanosoma cruzi bound to NADP

• PDB DOI: https://doi.org/10.2210/pdb4GIE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi strain CL Brener
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-08 Released: 2012-08-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.136 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP.

Moen, S.O., Fairman, J.W., Barnes, S.R., Sullivan, A., Nakazawa-Hewitt, S., Van Voorhis, W.C., Staker, B.L., Lorimer, D.D., Myler, P.J., Edwards, T.E.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 609-614

• PubMed: 25945716 
• DOI: https://doi.org/10.1107/S2053230X15006883
• Primary Citation Related Structures: 
  4F40, 4FZI, 4G5D, 4GIE


• PubMed Abstract: 
  

  The crystal structures of prostaglandin F synthase (PGF) from both Leishmania major and Trypanosoma cruzi with and without their cofactor NADP have been determined to resolutions of 2.6 Å for T. cruzi PGF, 1.25 Å for T. cruzi PGF with NADP, 1.6 Å for L. major PGF and 1.8 Å for L. major PGF with NADP. These structures were determined by molecular replacement to a final R factor of less than 18.6% (Rfree of less than 22.9%). PGF in the infectious protozoa L. major and T. cruzi is a potential therapeutic target.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Disease, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 34.39 kDa 
• Atom Count: 2,854 
• Modeled Residue Count: 288 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin F synthase	A	290	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053511287.49 EC: 1.1.1.188 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for Q4DJ07 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DJ07  Go to UniProtKB:  Q4DJ07

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.136 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.119 (Depositor) 
• R-Value Observed: 0.120 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GIE

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.54	α = 90
b = 50.34	β = 94.23
c = 37.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2015-06-03
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description