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- PDB-7qyh: Structure of plasmepsin II in complex with 2-aminoquinazolin-4(3H... -

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Basic information

Entry
Database: PDB / ID: 7qyh
TitleStructure of plasmepsin II in complex with 2-aminoquinazolin-4(3H)-one based open-flap inhibitor
ComponentsPlasmepsin II
KeywordsHYDROLASE / Eukaryotic aspartic protease / malaria / plasmepsin
Function / homology
Function and homology information


MHC class II antigen presentation / hemoglobin catabolic process / cytostome / plasmepsin II / vacuolar lumen / Neutrophil degranulation / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / lysosome / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-I0J / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsBobrovs, R. / Jaudzems, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/2/18/379European Union
Citation
Journal: J.Chem.Inf.Model. / Year: 2022
Title: Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials.
Authors: Bobrovs, R. / Basens, E.E. / Drunka, L. / Kanepe, I. / Matisone, S. / Velins, K.K. / Andrianov, V. / Leitis, G. / Zelencova-Gopejenko, D. / Rasina, D. / Jirgensons, A. / Jaudzems, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,0305
Polymers147,6384
Non-polymers3921
Water00
1
A: Plasmepsin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3012
Polymers36,9101
Non-polymers3921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasmepsin II


Theoretical massNumber of molelcules
Total (without water)36,9101
Polymers36,9101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Plasmepsin II


Theoretical massNumber of molelcules
Total (without water)36,9101
Polymers36,9101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Plasmepsin II


Theoretical massNumber of molelcules
Total (without water)36,9101
Polymers36,9101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.821, 274.066, 273.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Plasmepsin II / Plasmepsin 2


Mass: 36909.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PMII, PF3D7_1408000 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I6V3, plasmepsin II
#2: Chemical ChemComp-I0J / 2-azanyl-3-[[(2~{R})-oxolan-2-yl]methyl]-7-(5-phenylpentyl)quinazolin-4-one


Mass: 391.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N3O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 4.5 Å3/Da / Density % sol: 72.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M citric acid, pH 4.5, 0.3M ammonium acetate, 25% PEG 4000, protein 10 mg/mL, vapour diffusion, sitting drop, time 4-8 weeks

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.33→137.03 Å / Num. obs: 15336 / % possible obs: 86.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 68.32 Å2 / CC1/2: 0.987 / Net I/σ(I): 4.6
Reflection shellResolution: 3.33→4.03 Å / Num. unique obs: 767 / CC1/2: 0.592

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z22

4z22


Resolution: 3.33→137.03 Å / SU ML: 0.6419 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.6097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3358 834 5.44 %
Rwork0.3104 14494 -
obs0.3117 15328 38.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.9 Å2
Refinement stepCycle: LAST / Resolution: 3.33→137.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10420 0 29 0 10449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013610720
X-RAY DIFFRACTIONf_angle_d1.624214595
X-RAY DIFFRACTIONf_chiral_restr0.11271641
X-RAY DIFFRACTIONf_plane_restr0.00651893
X-RAY DIFFRACTIONf_dihedral_angle_d11.00813838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.33-3.540.364450.3424121X-RAY DIFFRACTION1.92
3.54-3.810.3371150.3464222X-RAY DIFFRACTION3.65
3.81-4.20.3765430.3488835X-RAY DIFFRACTION13.46
4.2-4.80.31581530.30322334X-RAY DIFFRACTION37.66
4.8-6.050.33472740.32934451X-RAY DIFFRACTION71.31
6.05-137.030.34143440.29936531X-RAY DIFFRACTION99.85

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