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- PDB-1lf3: CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1lf3
TitleCRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM IN COMPLEX WITH INHIBITOR EH58
Componentsplasmepsin 2
KeywordsHYDROLASE / plasmepsin / plasmodium falciparum / aspartic protease
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
Chem-EH5 / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAsojo, O.A. / Gulnik, S.V. / Afonina, E. / Yu, B. / Ellman, J.A. / Haque, T.S. / Silva, A.M.
CitationJournal: 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
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: plasmepsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9302
Polymers37,1241
Non-polymers8061
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: plasmepsin 2
hetero molecules

A: plasmepsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8604
Polymers74,2482
Non-polymers1,6122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5660 Å2
ΔGint-46 kcal/mol
Surface area26420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.411, 39.904, 91.409
Angle α, β, γ (deg.)90.00, 105.11, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein plasmepsin 2


Mass: 37123.941 Da / Num. of mol.: 1 / Fragment: Residues 123-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: PET 22B (NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P46925, plasmepsin II
#2: Chemical ChemComp-EH5 / N-(1-BENZYL-3-{[3-(1,3-DIOXO-1,3-DIHYDRO-ISOINDOL-2-YL)-PROPIONYL]-[2-(HEXAHYDRO-BENZO[1,3]DIOXOL-5-YL)-ETHYL]-AMINO}-2-HYDROXY-PROPYL)-4-BENZYLOXY-3,5-DIMETHOXY-BENZAMIDE


Mass: 805.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H51N3O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 298 K / Details: 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMTris-HCl1droppH7.0
37 mMinhibitor1drop
410 %(v/v)DMSO1drop
50.1 Mcitric acid1reservoirpH4.5
60.3 Mammonium acetate1reservoir
725 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 9126 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / Rsym value: 0.28 / % possible all: 90
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 18608 / % possible obs: 93 % / Rmerge(I) obs: 0.0669
Reflection shell
*PLUS
% possible obs: 87.1 % / Rmerge(I) obs: 0.322

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SME

1sme


Resolution: 2.7→17.76 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1165627.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 447 4.9 %RANDOM
Rwork0.178 ---
obs0.178 9125 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7997 Å2 / ksol: 0.278511 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å21.13 Å2
2--6.67 Å20 Å2
3----4.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→17.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 59 52 2730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 64 4.6 %
Rwork0.276 1313 -
obs--80.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.9
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.9 Å

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