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- PDB-8jcq: Crystal structure of calotropain FI from Calotropis gigantea -

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Basic information

Entry
Database: PDB / ID: 8jcq
TitleCrystal structure of calotropain FI from Calotropis gigantea
ComponentsProcerain
KeywordsHYDROLASE / plant protease / cystein peptidase / latex / Calotropis gigantea / endopeptidase
Function / homologyChem-E64
Function and homology information
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKumar, A. / Jamdar, S.N. / Srivastava, G. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Crystal Structure of Papain-Like Cysteine Protease, Calotropain FI, Purified from the Latex of Calotropis gigantea.
Authors: Jamdar, S.N. / Kumar, A. / Srivastava, G. / Makde, R.D.
History
DepositionMay 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 2.0Nov 20, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_database_related / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_asym / struct_conn / struct_conn_type / struct_keywords
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.title / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_database_related.details / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct.title / _struct_keywords.text
Description: Sequence discrepancy
Details: The polypeptide sequence is updated in revised entry
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Apr 23, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Procerain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7912
Polymers23,4311
Non-polymers3601
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.616, 121.272, 61.006
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 Procerain


Mass: 23430.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: natural isolated / Source: (natural) Calotropis gigantea (mudar) / Variant: Local / Strain: Mumbai / Tissue: leaf latex
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 9
Details: 0.1 M TBG (Tartrate, Bis-Tris, Glycylglycin) buffer pH 6.0 25% PEG 1500

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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: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2021 / Details: Mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.25→43.01 Å / Num. obs: 68894 / % possible obs: 98.1 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 19.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2626 / CC1/2: 0.826 / Rpim(I) all: 0.257 / Rrim(I) all: 0.535 / % possible all: 76.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RESOLVEmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→43.01 Å / SU ML: 0.104 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 3387 4.92 %
Rwork0.1648 65507 -
obs0.1657 68894 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.46 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 22 275 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01281757
X-RAY DIFFRACTIONf_angle_d1.24012384
X-RAY DIFFRACTIONf_chiral_restr0.1059250
X-RAY DIFFRACTIONf_plane_restr0.0112312
X-RAY DIFFRACTIONf_dihedral_angle_d16.1006659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.24561000.26442091X-RAY DIFFRACTION74.96
1.27-1.290.25171230.2272423X-RAY DIFFRACTION87.94
1.29-1.310.21491270.21452549X-RAY DIFFRACTION93.8
1.31-1.330.19611420.20242683X-RAY DIFFRACTION97.68
1.33-1.350.22461530.19252740X-RAY DIFFRACTION99.62
1.35-1.380.20231520.182757X-RAY DIFFRACTION100
1.38-1.40.19121440.18592743X-RAY DIFFRACTION99.97
1.4-1.430.21081520.18472765X-RAY DIFFRACTION99.97
1.43-1.460.20591400.19492738X-RAY DIFFRACTION100
1.46-1.50.19691150.18532794X-RAY DIFFRACTION99.97
1.5-1.540.20931280.16382779X-RAY DIFFRACTION99.97
1.54-1.580.18261410.16152769X-RAY DIFFRACTION100
1.58-1.620.18441730.15832745X-RAY DIFFRACTION100
1.62-1.680.18211230.15362785X-RAY DIFFRACTION100
1.68-1.740.17331710.15912745X-RAY DIFFRACTION100
1.74-1.810.19131190.16672800X-RAY DIFFRACTION100
1.81-1.890.17721700.16252759X-RAY DIFFRACTION100
1.89-1.990.16341530.15982781X-RAY DIFFRACTION100
1.99-2.110.17691290.14982805X-RAY DIFFRACTION100
2.11-2.270.17231420.15852809X-RAY DIFFRACTION100
2.27-2.50.18861620.16432792X-RAY DIFFRACTION100
2.5-2.870.18671570.16882817X-RAY DIFFRACTION100
2.87-3.610.16081460.16222838X-RAY DIFFRACTION100
3.61-43.010.19721250.15513000X-RAY DIFFRACTION99.87
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)
12.739331136220.954838621596-0.280850944852.154412278350.2875542425921.65606025662-0.00855133936855-0.0392759020127-0.356480348357-0.073176458173-0.037896774774-0.0824867520247-0.01091550113340.02140542405950.05397168717570.09624277686580.002132637730980.009049165282820.07275191652320.01561880232570.11274430912117.877781962218.1089678645-2.28033088864
25.040298223862.226741751190.5220806738941.998771463850.8511131818861.73942122765-0.1113571350870.139144266667-0.0800401424589-0.2071439012930.0919557317181-0.112221052086-0.2323597553090.0358016815660.03299637807590.11715088177-0.003660017945330.0007964662915280.08833378950580.01151968303120.084889608257825.402565439126.6083894123-5.44036759948
32.515891880971.163488656320.50768314350.9037179510290.042579696822.584653836910.368538433824-0.7230778276550.3359700251680.27461913366-0.293515959234-0.00376451905107-0.3164141510930.5026296211790.03199121067070.155706306562-0.06565104079425.42967092683E-50.279552836565-0.02312021086940.080627242001525.191752530531.68416718696.44849017511
45.728131573110.3622787420580.9766329895333.76589291012-1.06162991892.2419662841-0.03909191000190.0295640293358-0.392750792261-0.0909877560604-0.0299126763253-0.286494036985-0.023855451450.2203621500710.05987165465850.107282272679-0.02152263079880.02128021113280.127727276890.00284463564290.140193287734.333459465428.1606197972-3.41274449867
57.763913271542.30697081559-4.83631397141.80947643603-2.188306280615.455908003840.07945368114360.07680282817160.3247681857680.01200702790.1131062283610.142113756592-0.0625599703869-0.00818178344102-0.162665934840.1302802822640.00538242807611-0.02212261377790.100549472232-0.007738103092580.097771240441518.262348404533.0940365035-3.39523907087
62.53974530998-0.5382323109340.6538338046731.20645542645-0.205319776241.465558272530.0434825091593-0.362041047022-0.3116884056370.2540858820410.01190982547220.0414783108892-0.0224231532461-0.0942486085808-0.06337571744550.134245278056-0.00922932900128-0.001159281984360.1242575371110.04866593759230.11782250050411.618541947117.17562036569.02552169608
71.339880640630.5401373324760.9678748320911.887231564191.072699193874.397906127450.0520819417766-0.442302854597-0.4713465521290.397284832812-0.0688778766396-0.07363358837880.1428557279090.16350773807-0.03897479877880.211038222467-0.0100963899848-0.05528142089960.2227910033010.1242920454080.31364138191520.04705283437.060763556913.1701442553
81.317719157190.7538175145630.05748945159753.025477956640.1972421231250.555788703334-0.0136048473643-0.0682941550775-0.3343635540020.0187382923453-0.055811159728-0.1238594917960.06837426976580.02706555518190.07109496537380.1128477701440.005852545538790.005557813145460.09089550863420.03670028033790.19105524516216.44597258099.025433468482.77912239848
92.3254360336-0.483668486186-0.2541698702672.133514383040.7292158707781.61035855186-0.097706677139-0.362218824985-0.4274966306260.267581439441-0.003309100633280.08242227157040.173131946428-0.05089549921520.08017071241870.15768157966-0.005242674881240.0008083733952160.1488697335290.0831810547120.20819167137110.62970856239.072413443849.9083999805
101.69205743279-0.4724425088710.3427291316154.3694752204-2.248205164351.570316553210.0618795976783-0.0770468739643-0.0874757831771-0.06066114085390.04212846876560.1252643320950.117675243064-0.00447557940077-0.0571392084020.133799598263-0.00210585809269-0.0007187739996320.142417775320.007664607128010.10480352963512.631162656622.86878338276.45520386512
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 124 through 165 )124 - 1651 - 42
22chain 'A' and (resid 166 through 181 )166 - 18143 - 58
33chain 'A' and (resid 182 through 203 )182 - 20359 - 80
44chain 'A' and (resid 204 through 223 )204 - 22381 - 100
55chain 'A' and (resid 224 through 234 )224 - 234101 - 111
66chain 'A' and (resid 235 through 263 )235 - 263112 - 140
77chain 'A' and (resid 264 through 279 )264 - 279141 - 156
88chain 'A' and (resid 280 through 310 )280 - 310157 - 187
99chain 'A' and (resid 311 through 323 )311 - 323188 - 200
1010chain 'A' and (resid 324 through 337 )324 - 337201 - 214

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