3F9Q

Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.,Sect.D 65: 294-296

  • DOI: 10.1107/S0907444908041632

  • 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 ...

    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.


    Related Citations: 
    • Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum.
      Asojo, O.A.,Gulnik, S.V.,Afonina, E.,Yu, B.,Ellman, J.A.,Haque, T.S.,Silva, A.M.
      (2003) J.Mol.Biol. 327: 173


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasmepsin-2
A
329Plasmodium falciparumMutation(s): 1 
EC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Go to UniProtKB:  P46925
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 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 = 90.00
b = 39.567β = 105.54
c = 90.532γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-16
    Type: Atomic model