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- PDB-3f9q: Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum. -

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Basic information

Entry
Database: PDB / ID: 3f9q
TitleRe-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.
ComponentsPlasmepsin-2
KeywordsHYDROLASE / Aspartyl protease / Glycoprotein / Protease / Vacuole / Zymogen
Function / homology
Function and homology information


cytostome / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRobbins, A.H. / Mckenna, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.
Authors: Robbins, A.H. / Dunn, B.M. / Agbandje-McKenna, M. / McKenna, R.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum.
Authors: Asojo, O.A. / Gulnik, S.V. / Afonina, E. / Yu, B. / Ellman, J.A. / Haque, T.S. / Silva, A.M.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmepsin-2


Theoretical massNumber of molelcules
Total (without water)36,9101
Polymers36,9101
Non-polymers00
Water3,819212
1
A: Plasmepsin-2

A: Plasmepsin-2


Theoretical massNumber of molelcules
Total (without water)73,8192
Polymers73,8192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1830 Å2
ΔGint-16 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.659, 39.567, 90.532
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

Details1

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Components

#1: Protein Plasmepsin-2 / Aspartic hemoglobinase II / PFAPD


Mass: 36909.617 Da / Num. of mol.: 1 / Mutation: M205S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: P46925, plasmepsin II
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→19.8 Å / Num. obs: 29457 / Observed criterion σ(F): 0

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Processing

SoftwareName: CNS / Version: 1.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LF4

1lf4


Resolution: 1.9→19.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1443 -Random
Rwork0.212 ---
all-28753 --
obs-28457 99 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5 Å28.7 Å2-3.6 Å2
2--0 Å21.9 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.03 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 0 212 2780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.8

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