Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.212 

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This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1107/S0907444908041632
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmepsin-2329Plasmodium falciparumMutation(s): 1 
Find proteins for P46925 (Plasmodium falciparum (isolate HB3))
Explore P46925 
Go to UniProtKB:  P46925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46925
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.212 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.659α = 90
b = 39.567β = 105.54
c = 90.532γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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