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- PDB-1lee: CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1lee
TitleCRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WITH INHIBITOR RS367
ComponentsPlasmepsin 2
KeywordsHYDROLASE / plasmepsin / aspartic protease / plasmodium falciparum
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-R36 / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAsojo, O.A. / Afonina, E. / Gulnik, S.V. / Yu, B. / Erickson, J.W. / Randad, R. / Mehadjed, D. / Silva, A.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 A in complex with the inhibitors rs367 and rs370.
Authors: Asojo, O.A. / Afonina, E. / Gulnik, S.V. / Yu, B. / Erickson, J.W. / Randad, R. / Medjahed, D. / Silva, A.M.
#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
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6122
Polymers37,0801
Non-polymers5321
Water6,089338
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)75,2234
Polymers74,1602
Non-polymers1,0632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area6880 Å2
ΔGint-35 kcal/mol
Surface area23990 Å2
MethodPISA
3
A: Plasmepsin 2
hetero molecules

A: Plasmepsin 2
hetero molecules

A: Plasmepsin 2
hetero molecules

A: Plasmepsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,4468
Polymers148,3194
Non-polymers2,1274
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)75.890, 84.830, 123.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 37079.824 Da / Num. of mol.: 1 / Fragment: Residues 123-453 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P46925, plasmepsin II
#2: Chemical ChemComp-R36 / 4-AMINO-N-{4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-1-ISOBUTYL-5-PHENYL-PENTYL}-BENZAMIDE


Mass: 531.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H41N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 293 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMTris-HCl1droppH7.0
37 mMinhibitor1drop
410 %DMSO1drop
50.10 Msodium citrate1reservoirpH6.0
60.20 Mphosphate1reservoir
718 %ammonium sulfate1reservoir
85 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 26322 / Num. obs: 23619 / % possible obs: 71 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3 / Rsym value: 0.22 / % possible all: 33
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 26322 / % possible obs: 71 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 33 % / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2

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Processing

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

1sme


Resolution: 1.9→34.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 600592.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1113 5 %RANDOM
Rwork0.236 ---
obs-22291 70.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.482127 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--4.65 Å20 Å2
3----3.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 39 338 2994
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
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_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.51.5
X-RAY DIFFRACTIONc_mcangle_it3.712
X-RAY DIFFRACTIONc_scbond_it29.482
X-RAY DIFFRACTIONc_scangle_it8.572.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 107 5.1 %
Rwork0.294 2007 -
obs--40.7 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.8
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.264

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