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- PDB-4z22: structure of plasmepsin II from Plasmodium Falciparum complexed w... -

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Basic information

Entry
Database: PDB / ID: 4z22
Titlestructure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor DR718A
ComponentsPlasmepsin-2
KeywordsHYDROLASE / plasmepsin II / malaria / inhibitor
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 / 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
Chem-4KG / Plasmepsin II / Plasmepsin-2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsRecacha, R. / Leitans, J. / Tars, K. / Jaudzems, K.
Citation
Journal: J.Med.Chem. / Year: 2016
Title: Fragment-Based Discovery of 2-Aminoquinazolin-4(3H)-ones As Novel Class Nonpeptidomimetic Inhibitors of the Plasmepsins I, II, and IV.
Authors: Rasina, D. / Otikovs, M. / Leitans, J. / Recacha, R. / Borysov, O.V. / Kanepe-Lapsa, I. / Domraceva, I. / Pantelejevs, T. / Tars, K. / Blackman, M.J. / Jaudzems, K. / Jirgensons, A.
#1: Journal: Nat. Struct. Biol. / Year: 1999
Title: Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from plasmodium falciparum.
Authors: Bernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N.
#2: Journal: J. Mol. Biol. / Year: 2003
Title: Structural insights into the activation of P. vivax plasmepsin.
Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.
History
DepositionMar 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmepsin-2
B: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6144
Polymers73,8192
Non-polymers7952
Water1,29772
1
A: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3072
Polymers36,9101
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3072
Polymers36,9101
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.450, 174.690, 138.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

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Components

#1: Protein Plasmepsin-2 / plasmepsin II


Mass: 36909.617 Da / Num. of mol.: 2 / Fragment: UNP residues 125-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFAG_05140 / Production host: Escherichia coli (E. coli) / References: UniProt: W7FL77, UniProt: P46925*PLUS
#2: Chemical ChemComp-4KG / 2-amino-7-phenyl-3-{[(2R,5S)-5-phenyltetrahydrofuran-2-yl]methyl}quinazolin-4(3H)-one


Mass: 397.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M CITRIC ACID, PH 4.5, 0.4M AMMONIUM ACETATE, 21% PEG 3350, PROTEIN 10 MG/ML, 10 MM INHIBITOR (in 100% DMSO)
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.62→87.345 Å / Num. all: 19551 / Num. obs: 19551 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.104 / Rsym value: 0.088 / Net I/av σ(I): 7.281 / Net I/σ(I): 9.1 / Num. measured all: 66480
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.62-2.7630.5811.3815327140.3860.581296.3
2.76-2.933.20.3512.2840826470.230.3513.299.5
2.93-3.133.40.2183.5864025200.1370.2184.899.9
3.13-3.383.60.1375.6840423660.0840.1377.2100
3.38-3.713.60.0918.2779921760.0550.09110.2100
3.71-4.143.60.06510.6714319860.040.06513.2100
4.14-4.783.60.05510.9628317640.0330.05517100
4.78-5.863.50.0718.7528814990.0430.07116.5100
5.86-8.293.50.05511.2415011890.0340.05516100
8.29-41.6643.20.02716.522126900.0180.02719.499

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACT2.62data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJU

2bju


Resolution: 2.62→41.664 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 983 5.04 %Random selection
Rwork0.2058 ---
obs0.2082 19515 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→41.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 60 72 5342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035464
X-RAY DIFFRACTIONf_angle_d0.8147447
X-RAY DIFFRACTIONf_dihedral_angle_d11.6221951
X-RAY DIFFRACTIONf_chiral_restr0.031831
X-RAY DIFFRACTIONf_plane_restr0.004950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.75810.35511380.29092511X-RAY DIFFRACTION96
2.7581-2.93090.3121210.27462621X-RAY DIFFRACTION99
2.9309-3.15710.33721330.25052628X-RAY DIFFRACTION100
3.1571-3.47470.29631530.22232638X-RAY DIFFRACTION100
3.4747-3.97710.2691520.19772641X-RAY DIFFRACTION100
3.9771-5.00940.18951340.16142680X-RAY DIFFRACTION100
5.0094-41.66890.2051520.18712813X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8478-0.64950.30072.11550.06521.1389-0.04890.37710.215-0.0839-0.04970.0583-0.15480.03680.07210.27930.0169-0.00460.27710.01190.2088-4.5084-0.4937-18.0877
23.505-0.55670.19612.9553-1.2351.64250.06010.03-0.1417-0.7803-0.4597-0.55820.70890.37040.14610.76560.32050.34810.47850.19690.60312.189341.2412-17.3825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:329)
2X-RAY DIFFRACTION2(chain B and resseq 1:329)

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