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- PDB-1me6: CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLA... -

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Basic information

Entry
Database: PDB / ID: 1me6
TitleCRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR
ComponentsPlasmepsin II
KeywordsHYDROLASE / Protein-ligand 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
Chem-IVS / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFreire, E. / Nezami, A.G. / Amzel, L.M.
CitationJournal: TO BE PUBLISHED
Title: CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASE FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR
Authors: Freire, E. / Nezami, A.G. / Amzel, L.M.
History
DepositionAug 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: 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 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmepsin II
B: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8794
Polymers73,9072
Non-polymers9712
Water2,162120
1
A: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4392
Polymers36,9541
Non-polymers4861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4392
Polymers36,9541
Non-polymers4861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Plasmepsin II
hetero molecules

B: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8794
Polymers73,9072
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4820 Å2
ΔGint-37 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.930, 141.930, 97.820
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: 36953.734 Da / Num. of mol.: 2 / Fragment: RESIDUES 125-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF00026 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLYS / References: UniProt: P46925, plasmepsin II
#2: Chemical ChemComp-IVS / 3-HYDROXY-6-METHYL-4-(3-METHYL-2-(3-METHYL-2-(3-METHYL-BUTYRYLAMINO)-BUTYRYLAMINO)-BUTYRYLAMINO)-HEPTANOIC ACID ETHYL ESTER


Mass: 485.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H47N3O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.85 Å3/Da / Density % sol: 68.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 18, 2001 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 28346 / Num. obs: 28346 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SME

1sme


Resolution: 2.7→50 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1441 5 %Random
Rwork0.2141 ---
all-31557 --
obs-26905 89.8 %-
Displacement parametersBiso mean: 28.128 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 68 120 5402
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.57558
X-RAY DIFFRACTIONc_bond_d0.007881
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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