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- PDB-1sme: PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALC... -

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Basic information

Entry
Database: PDB / ID: 1sme
TitlePLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A
Components
  • PLASMEPSIN II
  • Pepstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTYL PROTEINASE / ASPARTIC PROTEINASE / ASPARTYL PROTEASE / 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
Pepstatin / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsSilva, A.M. / Lee, A.Y. / Gulnik, S.V. / Goldberg, D.E. / Erickson, J.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum.
Authors: Silva, A.M. / Lee, A.Y. / Gulnik, S.V. / Maier, P. / Collins, J. / Bhat, T.N. / Collins, P.J. / Cachau, R.E. / Luker, K.E. / Gluzman, I.Y. / Francis, S.E. / Oksman, A. / Goldberg, D.E. / Erickson, J.W.
History
DepositionJun 11, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMEPSIN II
B: PLASMEPSIN II
C: Pepstatin
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)75,2794
Polymers75,2794
Non-polymers00
Water2,072115
1
A: PLASMEPSIN II
C: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,6402
Polymers37,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area14230 Å2
MethodPISA
2
B: PLASMEPSIN II
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,6402
Polymers37,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-10 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.100, 142.100, 97.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PLASMEPSIN II


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)
Plasmid: PET VECTOR 22B (NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P46925, plasmepsin II
#2: Protein/peptide Pepstatin


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 Mphosphate1reservoir
347 %1reservoir(NH4)2SO4

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 23526 / % possible obs: 77 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.94
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 22465 / Num. measured all: 63000

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.7→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.195 --
obs0.195 22465 74.3 %
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 0 115 5425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.82 Å
RfactorNum. reflection% reflection
Rwork0.26 2004 -
obs--53.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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