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- PDB-1ls5: Crystal structure of plasmepsin IV from P. falciparum in complex ... -

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Basic information

Entry
Database: PDB / ID: 1ls5
TitleCrystal structure of plasmepsin IV from P. falciparum in complex with pepstatin A
Components
  • Pepstatin
  • plasmepsin IV
KeywordsHYDROLASE/HYDROLASE INHIBITOR / EUKARYOTIC ASPARTIC PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


MHC class II antigen presentation / hemoglobin catabolic process / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / Neutrophil degranulation / food vacuole / aspartic-type endopeptidase activity / lysosome / proteolysis / membrane
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 IV
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJun 12, 2002ID: 1JGF
Revision 1.0Jun 12, 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 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,3434
Polymers75,3434
Non-polymers00
Water50428
1
A: plasmepsin IV
C: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area14380 Å2
MethodPISA
2
B: plasmepsin IV
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-10 kcal/mol
Surface area14230 Å2
MethodPISA
3
A: plasmepsin IV
B: plasmepsin IV
C: Pepstatin
D: Pepstatin

A: plasmepsin IV
B: plasmepsin IV
C: Pepstatin
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)150,6858
Polymers150,6858
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area13410 Å2
ΔGint-93 kcal/mol
Surface area49190 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-43 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.930, 101.930, 123.389
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 IV


Mass: 36985.457 Da / Num. of mol.: 2
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: Q8IM16
#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.: 28 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growpH: 5.5 / Details: pH 5.50

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2000
RadiationMonochromator: DOUBLE FOCUSING MIRROR SYSTEM / Protocol: 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. obs: 15253 / % possible obs: 79 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.096 / Rsym value: 0.083 / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PLASMEPSIN II, PDB ENTRY 1SME

1sme


Resolution: 2.8→10 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.29 650 5 %RANDOM
Rwork0.22 ---
obs-12147 --
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 0 28 5342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
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

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