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- PDB-7ei0: Crystal structure of falcipain 2 from 3D7 strain -

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Basic information

Entry
Database: PDB / ID: 7ei0
TitleCrystal structure of falcipain 2 from 3D7 strain
ComponentsCysteine proteinase falcipain 2a
KeywordsHYDROLASE / malaria / plasmodium / protease / falcipain 2 / drug target
Function / homology
Function and homology information


food vacuole / proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / extracellular space / membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Falcipain-2a
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChakraborty, S. / Biswas, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain.
Authors: Chakraborty, S. / Alam, B. / Biswas, S.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine proteinase falcipain 2a
B: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,58614
Polymers54,5252
Non-polymers1,06012
Water95553
1
A: Cysteine proteinase falcipain 2a
hetero molecules

B: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,58614
Polymers54,5252
Non-polymers1,06012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_454x-1/2,-y+1/2,-z-1/41
Buried area3450 Å2
ΔGint-57 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.550, 115.550, 240.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 41 or resid 43 through 241))
21(chain B and (resid 1 through 41 or resid 43 through 241))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSER(chain A and (resid 1 through 41 or resid 43 through 241))AA1 - 411 - 41
12TRPTRPGLUGLU(chain A and (resid 1 through 41 or resid 43 through 241))AA43 - 24143 - 241
21GLNGLNSERSER(chain B and (resid 1 through 41 or resid 43 through 241))BB1 - 411 - 41
22TRPTRPGLUGLU(chain B and (resid 1 through 41 or resid 43 through 241))BB43 - 24143 - 241

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine proteinase falcipain 2a /


Mass: 27262.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1115700 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8I6U4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Non-polymers , 6 types, 65 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 7.37 Å3/Da / Density % sol: 83.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: ethylene glycol, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→48.48 Å / Num. obs: 23265 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.061 / Rrim(I) all: 0.228 / Net I/σ(I): 10.9 / Num. measured all: 319821 / Scaling rejects: 50
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.6713.51.9146308446610.7140.5391.9891.8100
9-48.48120.0421696214170.9990.0120.04346.899.3

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BPF

3bpf


Resolution: 3.4→38.688 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 1151 4.98 %
Rwork0.2622 21971 -
obs0.2633 23122 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 316.21 Å2 / Biso mean: 136.1669 Å2 / Biso min: 1.06 Å2
Refinement stepCycle: final / Resolution: 3.4→38.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 144 53 4023
Biso mean--101.01 93.74 -
Num. residues----482
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1422X-RAY DIFFRACTION14.947TORSIONAL
12B1422X-RAY DIFFRACTION14.947TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4001-3.55470.37271560.38072661100
3.5547-3.7420.37431530.34562676100
3.742-3.97620.38661280.34292731100
3.9762-4.28290.36321250.3162270399
4.2829-4.71320.28881320.2736272599
4.7132-5.39360.31761450.26832737100
5.3936-6.78940.30331640.26542790100
6.7894-38.6880.19511480.18912948100
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)
16.9834-5.1875-1.75655.2488-0.61036.4487-0.568-0.1967-1.6969-0.3968-0.4918-1.29152.9971-1.34551.14741.772-0.26970.17141.20040.40931.9861-33.517-1.358-40.735
27.92362.14754.05243.81891.894810.1810.0071-1.1122-0.11520.4633-0.3797-0.38970.30690.31290.35050.79930.17290.04861.38340.53280.9501-21.79917.759-28.972
35.10991.8711-0.55337.86462.20178.6979-0.32350.3867-0.6416-1.277-0.011-0.83572.02730.82930.36711.03770.11360.04020.91370.41260.99-24.5117.364-42.224
45.70865.8969-3.49325.5782-1.80338.574-0.55111.90110.1062-2.217-0.2296-1.66670.47170.81990.54051.1449-0.00260.26891.54710.26621.324-18.78818.885-53.615
56.77681.73562.11895.94254.88624.4507-0.56710.4066-1.0643-0.2378-0.31620.51911.29590.98270.9880.9034-0.04570.12531.14780.19440.9319-31.22813.417-56.706
611.7313.01841.02119.5571-2.68535.232-0.1474-0.3498-0.7807-0.6345-0.00720.10240.52960.85070.37310.69990.13170.09830.94530.26670.5688-25.23513.415-45.948
73.4664-1.2237-2.78684.9921-1.77544.0312.5825-2.2494-0.34194.4442-0.99610.51811.5336-3.2646-1.39292.4017-0.8951-0.08412.31590.33131.3517-4.06618.9851.182
811.309715.5129-0.150519.8376-2.0875.8819-0.1880.528-0.9352-0.8220.414-1.132-0.1689-0.2516-0.2930.68750.1271-0.0051.37390.33150.887.03329.642-18.136
92.86128.41810.991811.3059-4.49355.58144.567-4.3668-3.38036.053-4.2098-2.9673-0.37911.3591-0.02192.0575-0.8617-0.91432.40290.78451.54981.8719.035-4.376
107.70690.5794-5.02449.9218-4.56895.4047-0.01970.8368-4.0571-1.43780.197-3.04054.44091.3443-0.16291.8462-0.07160.15561.9347-0.08732.16988.7164.999-20.64
111.08033.5592-1.2612.3075-0.8789-0.2341-0.576-0.2361-5.83990.6523-0.2716-8.05061.5843-0.24390.84431.7578-0.4681-0.11811.65810.2923.2951-4.3632.309-13.387
129.86399.7567-4.24919.86961.76393.60770.376-0.7712-3.3460.0345-0.4772-4.24610.1262-0.63420.10221.4873-0.0615-0.19411.5840.47612.37152.44512.993-13.849
131.99821.99431.99953.9759-2.5481.6359-0.85930.90151.6682-0.1857-0.87510.1721-1.61080.69730.27682.5447-0.7632-3.17361.99770.0715-3.5246-18.48530.102-41.658
141.99882.00612.00011.99029.74623.13143.2506-0.819-2.95021.7583-2.5634-2.8470.60290.3606-0.7552-0.72261.2608-2.33074.067-0.66620.9828-10.23713.628-39.078
151.39880.3678-0.7471.26111.3232.37620.2978-0.32121.9119-2.46980.5929-3.6403-0.68050.3122-0.41882.4050.4792-1.7372-3.9947-1.05944.2588-33.99219.937-54.803
161.999722.000422.00021.9988-16.737438.76520.2957-13.67167.059-6.2226-18.323713.19389.68736.9616-1.104-3.0607-2.5743-0.45293.6258-30.875-6.668-43.575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:23 )A1 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:124 )A24 - 124
3X-RAY DIFFRACTION3( CHAIN A AND RESID 125:157 )A125 - 157
4X-RAY DIFFRACTION4( CHAIN A AND RESID 158:173 )A158 - 173
5X-RAY DIFFRACTION5( CHAIN A AND RESID 174:203 )A174 - 203
6X-RAY DIFFRACTION6( CHAIN A AND RESID 204:241 )A204 - 241
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:23 )B1 - 23
8X-RAY DIFFRACTION8( CHAIN B AND RESID 24:124 )B24 - 124
9X-RAY DIFFRACTION9( CHAIN B AND RESID 125:150 )B125 - 150
10X-RAY DIFFRACTION10( CHAIN B AND RESID 151:173 )B151 - 173
11X-RAY DIFFRACTION11( CHAIN B AND RESID 174:203 )B174 - 203
12X-RAY DIFFRACTION12( CHAIN B AND RESID 204:241 )B204 - 241
13X-RAY DIFFRACTION13( CHAIN A AND RESID 301:301 )A301
14X-RAY DIFFRACTION14( CHAIN A AND RESID 302:302 )A302
15X-RAY DIFFRACTION15( CHAIN A AND RESID 304:304 )A304
16X-RAY DIFFRACTION16( CHAIN A AND RESID 306:306 )A306

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