3F9Q | pdb_00003f9q

Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.

• PDB DOI: https://doi.org/10.2210/pdb3F9Q/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-11-14 Released: 2009-03-10 
• Deposition Author(s): Robbins, A.H., Mckenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.

Robbins, A.H., Dunn, B.M., Agbandje-McKenna, M., McKenna, R.

(2009) Acta Crystallogr D Biol Crystallogr 65: 294-296

• PubMed: 19237752 
• DOI: https://doi.org/10.1107/S0907444908041632
• Primary Citation Related Structures: 
  3F9Q


• PubMed Abstract: 
  

  The carboxylate atoms of the two catalytic aspartic acid residues in aspartic proteases are nearly coplanar and in the uncomplexed form share an in-plane nucleophilic water molecule that is central to the mechanism of these enzymes. This note reports that while reviewing the electron-density maps derived from the deposited data for uncomplexed plasmepsin II from Plasmodium falciparum [Asojo et al. (2003), J. Mol. Biol. 327, 173-181; PDB code 1lf4], it was discovered that the aspartic acid residues in this structure should in fact be distinctly noncoplanar. The crystallographic model from the deposited coordinates has been re-refined against the 1.9 A resolution published diffraction data to an R(cryst) of 21.2% and an R(free) of 22.2%. The catalytic water molecule is present, but the plane of the carboxylate group of Asp214 is rotated by 66 degrees from its original position.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 36.91 kDa 
• Atom Count: 2,780 
• Modeled Residue Count: 325 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin-2	A	329	Plasmodium falciparum	Mutation(s): 1  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: 1.90 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.659	α = 90
b = 39.567	β = 105.54
c = 90.532	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Robbins, A.H., Mckenna, R.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary