5BWY | pdb_00005bwy

Structure of proplasmepsin II from Plasmodium falciparum, Space Group P43212

• PDB DOI: https://doi.org/10.2210/pdb5BWY/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-08 Released: 2015-12-16 
• Deposition Author(s): Recacha, R., Akopjana, I., Tars, K., Jaudzems, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.243 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins.

Recacha, R., Jaudzems, K., Akopjana, I., Jirgensons, A., Tars, K.

(2016) Acta Crystallogr F Struct Biol Commun 72: 659-666

• PubMed: 27599854 
• DOI: https://doi.org/10.1107/S2053230X16011663
• Primary Citation Related Structures: 
  5BWY, 5JOD


• PubMed Abstract: 
  

  Plasmepsin IV from Plasmodium falciparum (PM IV) is a promising target for the development of novel antimalarial drugs. Here, the crystal structure of the truncated zymogen of PM IV (pPM IV), consisting of the mature enzyme plus a prosegment of 47 residues, has been determined at 1.5 Å resolution. pPM IV presents the fold previously described for studied proplasmepsins, displaying closer similarities to proplasmepin IV from P. vivax (pPvPM) than to the other two proplasmepsins from P. falciparum. The study and comparison of the pPM IV structure with the proplasmepsin structures described previously provide information about the similarities and differences in the inactivation-activation mechanisms among the plasmepsin zymogens.

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Organizational Affiliation: 
• Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia.
Biomedical Research and Study Centre, Ratsupites 1, Riga, LV-1067, Latvia.

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: 42.37 kDa 
• Atom Count: 3,071 
• Modeled Residue Count: 376 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin-2	A	376	Plasmodium falciparum	Mutation(s): 0  Gene Names: PFAG_05140 EC: 3.4.23.39
UniProt
Find proteins for P46925 (Plasmodium falciparum (isolate HB3)) Explore P46925  Go to UniProtKB:  P46925

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.243 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.38	α = 90
b = 89.38	β = 90
c = 115.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Recacha, R., Akopjana, I., Tars, K., Jaudzems, K.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Data collection
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary