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- PDB-2r9b: Structural Analysis of Plasmepsin 2 from Plasmodium falciparum co... -

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Basic information

Entry
Database: PDB / ID: 2r9b
TitleStructural Analysis of Plasmepsin 2 from Plasmodium falciparum complexed with a peptide-based inhibitor
Components
  • Plasmepsin-2
  • peptide-based inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BETA FOLD ASPARTYL PROTEASE / GLYCOPROTEIN / VACUOLE / ZYMOGEN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
KPFS-(CH2-NH)-LQF peptidomimetic inhibitor of PfPM1 / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLiu, P. / Marzahn, M.R. / Robbins, A.H. / McKenna, R. / Dunn, B.M.
CitationJournal: Biochemistry / Year: 2009
Title: Recombinant plasmepsin 1 from the human malaria parasite plasmodium falciparum: enzymatic characterization, active site inhibitor design, and structural analysis.
Authors: Liu, P. / Marzahn, M.R. / Robbins, A.H. / Gutierrez-de-Teran, H. / Rodriguez, D. / McClung, S.H. / Stevens, S.M. / Yowell, C.A. / Dame, J.B. / McKenna, R. / Dunn, B.M.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Aug 17, 2011Group: Non-polymer description
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmepsin-2
C: peptide-based inhibitor
B: Plasmepsin-2
D: peptide-based inhibitor


Theoretical massNumber of molelcules
Total (without water)75,8404
Polymers75,8404
Non-polymers00
Water84747
1
A: Plasmepsin-2
C: peptide-based inhibitor


Theoretical massNumber of molelcules
Total (without water)37,9202
Polymers37,9202
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
MethodPISA
2
B: Plasmepsin-2
D: peptide-based inhibitor


Theoretical massNumber of molelcules
Total (without water)37,9202
Polymers37,9202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.489, 69.032, 53.578
Angle α, β, γ (deg.)90.000, 102.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

21B-336-

HOH

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Components

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


Mass: 36953.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: plasmepsin 2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P46925, plasmepsin II
#2: Protein/peptide peptide-based inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 966.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PEPTIDE-BASED INHIBITOR
References: KPFS-(CH2-NH)-LQF peptidomimetic inhibitor of PfPM1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6253
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop4.60.1 M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop4.60.1 M Sodium acetate trihydrate, 0.2 M Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2933vapor diffusion, hanging drop4.60.1 M Sodium acetate trihydrate, 0.2 M Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2007 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 19458 / Num. obs: 18700 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.098 / Χ2: 1.012 / Net I/σ(I): 9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.303 / Num. unique all: 1785 / Χ2: 0.811 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XDH

1xdh


Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1782 9.2 %Random
Rwork0.238 ---
all0.286 18700 --
obs0.271 16040 92.4 %-
Solvent computationBsol: 17.092 Å2
Displacement parametersBiso mean: 27.571 Å2
Baniso -1Baniso -2Baniso -3
1-3.312 Å20 Å20.407 Å2
2---2.351 Å20 Å2
3----0.961 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 0 47 5399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_deg1.37
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_DLU.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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