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- PDB-1m43: Crystal structure of PMII in complex with pepstatin a to 2.4 A -

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Basic information

Entry
Database: PDB / ID: 1m43
TitleCrystal structure of PMII in complex with pepstatin a to 2.4 A
Components
  • Pepstatin
  • plasmepsin II
KeywordsHYDROLASE/HYDROLASE INHIBITOR / plasmepsin II / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAsojo, O.A. / Silva, A.M. / Gulnik, S.
CitationJournal: To be Published
Title: Novel uncomplexed and complex structures of PM II, an aspartic protease from P. falciparum
Authors: Asojo, O.A. / Silva, A.M. / Gulnik, S.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,5314
Polymers75,5314
Non-polymers00
Water9,998555
1
A: plasmepsin II
C: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,7662
Polymers37,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-11 kcal/mol
Surface area14270 Å2
MethodPISA
2
B: plasmepsin II
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,7662
Polymers37,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-10 kcal/mol
Surface area14380 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-51 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.235, 142.235, 97.892
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 / Aspartic hemoglobinase II / PFAPD


Mass: 37079.824 Da / Num. of mol.: 2 / 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: 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.: 555 / 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: 3.85 Å3/Da / Density % sol: 68.08 %

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35751 / % possible obs: 79.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.0966 / Rsym value: 0.0966 / Net I/σ(I): 17.43
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 5117 / Rsym value: 0.26 / % possible all: 62.2

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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: 2.4→19.9 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1761 4.9 %RANDOM
Rwork0.197 ---
all0.198 ---
obs0.197 35694 79.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.7905 Å2 / ksol: 0.359847 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å21.66 Å20 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refine analyzeLuzzati coordinate error free: 0.34 Å / Luzzati sigma a free: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5330 0 0 555 5885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 201 4.3 %
Rwork0.292 4488 -
obs--63.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PEP.PARAMPEP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM

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