4F40

X-ray crystal structure of Apo prostaglandin f synthase from Leishmania major Friedlin

• PDB DOI:  https://doi.org/10.2210/pdb4F40/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-09 Released: 2012-06-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.180 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

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 of 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 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.91 kDa 
• Atom Count: 5,188 
• Modelled Residue Count: 560 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin f2-alpha synthase/D-arabinose dehydrogenase	A, B	288	Leishmania major	Mutation(s): 0  Gene Names: PGFS, LMJF_31_2150, P100/11E EC: 1.1.1.188 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for P22045 (Leishmania major) Explore P22045  Go to UniProtKB:  P22045

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], N [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.180 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34F40

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.55	α = 90
b = 34.59	β = 103.22
c = 107.2	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-06-13
  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