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- PDB-4ya8: structure of plasmepsin II from Plasmodium Falciparum complexed w... -

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Basic information

Entry
Database: PDB / ID: 4ya8
Titlestructure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor PG394
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
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-49W / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsRecacha, R. / Leitans, J. / Tars, K. / Jaudzems, K.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structures of plasmepsin II from Plasmodium falciparum in complex with two hydroxyethylamine-based inhibitors.
Authors: Recacha, R. / Leitans, J. / Akopjana, I. / Aprupe, L. / Trapencieris, P. / Jaudzems, K. / Jirgensons, A. / Tars, K.
#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
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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 1.3Nov 13, 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
C: Plasmepsin-2
D: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,35411
Polymers147,6384
Non-polymers2,7157
Water543
1
A: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5192
Polymers36,9101
Non-polymers6101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6123
Polymers36,9101
Non-polymers7022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7044
Polymers36,9101
Non-polymers7943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5192
Polymers36,9101
Non-polymers6101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.770, 177.770, 177.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid A
31chain C and segid A
41chain D and segid A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid AB0
311chain C and segid AC0
411chain D and segid AD0

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Components

#1: Protein
Plasmepsin-2 / Aspartic hemoglobinase II / PFAPD


Mass: 36909.617 Da / Num. of mol.: 4 / 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: Chemical
ChemComp-49W / N'-[(2S,3S)-3-hydroxy-1-phenyl-4-{[2-(pyridin-2-yl)propan-2-yl]amino}butan-2-yl]-N,N-dipropyl-5-(pyridin-1(2H)-yl)benzene-1,3-dicarboxamide


Mass: 609.801 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H47N5O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M sodium citrate, 80 % PEG 3350

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.301→177.77 Å / Num. all: 27601 / Num. obs: 27601 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.136 / Rsym value: 0.117 / Net I/av σ(I): 5.011 / Net I/σ(I): 7.5 / Num. measured all: 99396
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
3.3-3.483.60.6881.11440340530.4090.6881.899.1
3.48-3.693.60.4261.71370638460.250.4262.898.9
3.69-3.943.60.2861.61290236070.170.2864.198.9
3.94-4.263.60.1684.51203933430.0980.1686.498.1
4.26-4.673.60.1017.21109630710.0590.1019.497.8
4.67-5.223.60.0858.21007427650.0480.0851196.9
5.22-6.023.60.16.9877224100.0560.11196.4
6.02-7.383.70.0867.7753720450.0480.08612.794.8
7.38-10.443.70.03715.4575615720.0210.03716.294.2
10.44-59.2573.50.03511.231118890.0210.03518.492.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJU

2bju


Resolution: 3.301→56.216 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1408 5.11 %
Rwork0.1881 26138 -
obs0.1893 27546 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.13 Å2 / Biso mean: 84.6093 Å2 / Biso min: 36.38 Å2
Refinement stepCycle: final / Resolution: 3.301→56.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10414 0 198 3 10615
Biso mean--82.15 50.53 -
Num. residues----1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310936
X-RAY DIFFRACTIONf_angle_d0.80114879
X-RAY DIFFRACTIONf_chiral_restr0.0321651
X-RAY DIFFRACTIONf_plane_restr0.0041900
X-RAY DIFFRACTIONf_dihedral_angle_d11.4213872
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6276X-RAY DIFFRACTION7.273TORSIONAL
12B6276X-RAY DIFFRACTION7.273TORSIONAL
13C6276X-RAY DIFFRACTION7.273TORSIONAL
14D6276X-RAY DIFFRACTION7.273TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3005-3.41850.31321480.27882652280099
3.4185-3.55530.29611520.25562630278299
3.5553-3.71710.2541470.24262602274998
3.7171-3.9130.25371600.22762618277898
3.913-4.15810.25451490.19782604275398
4.1581-4.47910.17341280.16112623275197
4.4791-4.92960.16631350.14642636277197
4.9296-5.64230.18651150.16422603271896
5.6423-7.10650.22071260.19322609273595
7.1065-56.22390.17051480.1682561270992
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)
18.4089-5.15421.03828.19655.40727.8132-0.1508-0.46280.0010.11220.5997-0.8570.5299-0.0156-0.37690.7721-0.12720.1450.82930.03590.7814-49.1721-15.5242-19.3312
24.3824-0.08870.57054.48961.19922.33620.2169-0.07580.2499-0.0573-0.14360.2339-0.2828-0.0194-0.11850.6358-0.13620.07480.68380.1430.4893-63.1779-6.6061-19.1468
37.5015-3.65963.05327.6371-4.5099.2032-0.36610.3191-0.0667-0.16020.04-1.05010.2523-0.32740.27380.7634-0.1850.17610.70830.12360.5644-48.3705-16.1862-29.8171
44.5910.19430.38812.6033-1.48840.7995-0.00140.3544-0.2863-0.36080.0757-0.12720.4024-0.0156-0.05310.8457-0.01830.10540.5908-0.0410.5587-61.0015-34.0579-29.1844
53.86660.4414-2.53255.2911-3.78658.251-0.2672-0.77610.17950.10140.10710.60860.34290.32510.00970.8023-0.07990.12960.609-0.0250.9434-58.8016-42.5605-15.9219
61.95020.6819-1.43475.4546-3.62345.22580.13850.2134-0.0202-0.3258-0.1867-0.07020.16460.47310.08180.7078-0.10960.10310.64570.01180.5422-54.2611-31.8726-22.4595
74.8602-3.72390.27933.8229-0.58193.78780.2981-0.27910.03070.0559-0.14150.72240.8041-0.7424-0.17570.7908-0.465-0.04771.08890.0430.7516-96.7722-34.4888-19.5763
82.2388-0.5394-0.02574.5257-1.46572.27470.03780.2506-0.252-0.37020.05060.41220.3038-0.4874-0.09090.679-0.2336-0.08160.80090.00220.5733-91.0442-33.8095-24.2096
95.25320.8449-0.20868.33395.15333.39810.43121.02390.90640.32830.0669-0.32430.0892-0.7093-0.47540.7111-0.1009-0.05750.82590.26780.6916-86.3332-8.8538-25.5182
104.41082.5793.26253.34790.82576.0310.41380.42140.2116-0.5752-0.00260.0727-0.00930.3949-0.420.93070.05740.32220.7169-0.14040.9328-90.948-2.2852-12.0896
112.88911.42680.23894.56642.33444.45620.02880.1490.466-0.3425-0.03230.56480.0035-0.5549-0.01480.622-0.1562-0.0720.84250.19550.8005-95.5817-14.2999-25.0506
122.52670.1911-0.51953.0253-0.01434.2542-0.1488-0.1026-0.30160.07290.07410.21630.3177-0.29360.08730.50860.03290.01060.60470.14660.6987-64.25894.547-53.0516
132.1211.538-1.01395.6138-1.50893.5222-0.0002-0.23960.03270.6023-0.0680.6982-0.4333-0.23210.03940.62910.25150.06410.9436-0.09450.676-70.814426.5572-48.5201
142.76093.6887-1.81555.9651-0.64593.9044-0.0331-0.455-0.47220.9036-0.0439-0.07480.09180.51020.17720.93790.1839-0.12160.5769-0.04550.8165-58.360937.9732-48.2717
156.73292.2387-2.33384.2203-1.67813.02970.2379-0.70690.03450.2907-0.2140.464-0.8173-0.2557-0.19070.73170.2169-0.00170.78-0.00160.6258-65.764227.0152-45.8151
167.28486.8321-1.64167.0308-2.65432.47550.4815-0.13551.1443-1.2537-0.3331.01170.1774-0.36820.39590.86150.10920.09510.8968-0.10170.7212-33.6698-29.8648-1.9383
174.32641.3085-1.89116.4478-0.19725.613-0.08050.019-0.30260.14760.0502-0.18950.3326-0.08860.00780.6160.14640.16070.63010.00620.6377-32.4389-37.791112.3165
182.10111.2817-1.63294.3943-1.50692.81850.25850.43470.4626-2.0554-0.1605-1.49350.319-0.2474-0.03021.14650.24450.40680.8367-0.0580.7802-22.9789-30.8312-4.4679
193.0306-1.4364-1.72846.17722.10725.29290.3033-0.44490.0291-0.6249-0.2465-0.4328-0.41990.54320.08360.67550.03140.25860.61990.10380.7794-19.9738-12.08186.1602
202.3450.1650.98712.279-3.03214.92290.18560.18370.49640.96290.6986-0.17450.1304-0.7542-0.62390.90170.18810.19980.7202-0.00260.8587-37.5709-0.33946.0351
211.9463-1.3078-2.44732.25621.68533.10160.95471.62770.306-1.1955-0.6887-0.4151-1.2825-0.7918-0.13281.14350.36590.25171.09890.08610.8081-21.7592-8.3982-1.67
222.4495-3.23612.45388.1955-2.59292.61431.4617-0.08620.5553-1.8257-0.87741.34141.1708-0.6468-0.1711.08410.0647-0.0740.71350.0261.0827-41.3757-7.0391.3596
233.3405-0.8999-1.8724.80973.62876.7999-0.05050.1837-0.6808-0.9048-0.0275-0.7641-0.10920.56290.03580.73390.05970.25480.5108-0.01850.664-21.8931-18.57411.1696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 138 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 177 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 231 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 264 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 265 through 329 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 43 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 201 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 231 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 232 through 256 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 257 through 329 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 157 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 158 through 231 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 232 through 264 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 265 through 329 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 22 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 23 through 138 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 139 through 177 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 178 through 231 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 232 through 256 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 257 through 273 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 274 through 291 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 292 through 329 )D0

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