4G5D | pdb_00004g5d

X-ray crystal structure of Prostaglandin f synthase from Leishmania major Friedlin bound to NADPH

• PDB DOI: https://doi.org/10.2210/pdb4G5D/pdb

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


• Deposited: 2012-07-17 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: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (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 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: 65.87 kDa 
• Atom Count: 5,390 
• Modelled Residue Count: 565 
• 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 strain Friedlin	Mutation(s): 0  Gene Names: PGFS, LMJF_31_2150 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34G5D

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.66	α = 90
b = 34.59	β = 102.98
c = 106.95	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

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