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- PDB-6mrq: Structure of ToPI1 inhibitor from Tityus obscurus scorpion venom ... -

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Basic information

Entry
Database: PDB / ID: 6mrq
TitleStructure of ToPI1 inhibitor from Tityus obscurus scorpion venom in complex with trypsin
Components
  • Cationic trypsin
  • inhibitor from Tityus obscurus scorpion venom (TopI1)
Keywordshydrolase/hydrolase inhibitor / Inhibitor / Complex / Scorpion / Venom / HYDROLASE / toxin / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
Tityus (scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.288 Å
AuthorsFernandes, J.C. / Mourao, C.B.F. / Schwartz, E.F. / Barbosa, J.A.R.G.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)407625/2013-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309054/2014-1 Brazil
Fundacao de Apoio a Pesquisa do Distrito Federal (FAPDF)193.001.760/2017 Brazil
CitationJournal: J.Med.Chem. / Year: 2020
Title: Head-to-Tail Cyclization after Interaction with Trypsin: A Scorpion Venom Peptide that Resembles Plant Cyclotides.
Authors: Mourao, C.B.F. / Brand, G.D. / Fernandes, J.P.C. / Prates, M.V. / Bloch Jr., C. / Barbosa, J.A.R.G. / Freitas, S.M. / Restano-Cassulini, R. / Possani, L.D. / Schwartz, E.F.
History
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
I: inhibitor from Tityus obscurus scorpion venom (TopI1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0016
Polymers28,6732
Non-polymers3284
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The activity was confirmed by activity assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-45 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.817, 59.020, 79.085
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 24934.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#2: Protein/peptide inhibitor from Tityus obscurus scorpion venom (TopI1)


Mass: 3738.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tityus (scorpion)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes Sodium pH 7.5 1.5 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 4, 2016
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.28→27.65 Å / Num. obs: 55677 / % possible obs: 99.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05059 / Net I/σ(I): 18.26
Reflection shellResolution: 1.288→1.334 Å / Rmerge(I) obs: 0.8727 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 1.288→27.648 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.89
RfactorNum. reflection% reflection
Rfree0.1805 2000 3.59 %
Rwork0.165 --
obs0.1656 55671 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.288→27.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 16 297 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051955
X-RAY DIFFRACTIONf_angle_d0.832654
X-RAY DIFFRACTIONf_dihedral_angle_d12.272734
X-RAY DIFFRACTIONf_chiral_restr0.077295
X-RAY DIFFRACTIONf_plane_restr0.004333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2883-1.32050.34781280.35933443X-RAY DIFFRACTION90
1.3205-1.35620.25841410.28223772X-RAY DIFFRACTION100
1.3562-1.39610.27181430.24533828X-RAY DIFFRACTION100
1.3961-1.44120.26721420.2183820X-RAY DIFFRACTION100
1.4412-1.49270.2241420.20483819X-RAY DIFFRACTION100
1.4927-1.55240.22691430.19323815X-RAY DIFFRACTION100
1.5524-1.62310.22461420.17763842X-RAY DIFFRACTION100
1.6231-1.70870.16191430.16683831X-RAY DIFFRACTION100
1.7087-1.81570.18221440.16193848X-RAY DIFFRACTION100
1.8157-1.95580.18251440.15353867X-RAY DIFFRACTION100
1.9558-2.15260.15911440.15043876X-RAY DIFFRACTION100
2.1526-2.46390.16141460.15233897X-RAY DIFFRACTION100
2.4639-3.10360.16821450.15893924X-RAY DIFFRACTION100
3.1036-27.65430.16121530.14564089X-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)
12.8312-0.28140.10432.884-0.19062.0176-0.04040.06320.21850.1070.0199-0.0129-0.1740.05290.01030.10130.00160.00010.07740.03540.0813-7.43677.0896-12.6201
21.6217-0.98550.56344.5312-1.26181.00420.04480.27710.0546-0.1711-0.0502-0.08220.05030.11360.00540.09890.00620.00840.15490.00760.075-5.31091.2326-17.6435
31.8896-0.222-0.47764.4270.01383.53490.02790.19350.51070.0441-0.0854-0.2324-0.38140.29920.04910.0802-0.0302-0.02370.16840.04970.22791.97189.6789-13.7252
41.5020.4282-0.17222.2281-0.56131.58770.0123-0.2413-0.0480.33920.06950.18850.0219-0.1205-0.08170.16390.00990.03720.1420.02330.1062-12.8318-1.27-2.5657
54.35011.0928-1.14421.5097-0.10621.80040.1062-0.2135-0.1630.25360.01190.21590.1174-0.1696-0.09440.1732-0.00930.02030.1190.05710.1288-12.749-6.623-2.618
68.13152.7197-0.40747.7456-2.17926.3418-0.18190.3806-0.0102-0.1416-0.3105-1.02190.07841.15130.37670.12920.0204-0.02130.26650.06480.30079.5221-3.3596-10.853
75.06133.35134.82993.48695.24027.8961-0.25370.29430.2263-0.60510.07570.5738-0.049-0.38260.09810.1957-0.0706-0.08150.21330.05140.2067-20.4105-4.685-22.6332
85.3256-2.74691.35777.2173-2.82273.4626-0.02450.9406-0.4991-0.60150.4612-0.27830.38740.5405-0.41640.2005-0.0604-0.02190.3049-0.09720.2318-16.8133-11.8399-23.4521
93.2183.04333.33215.87781.34836.13490.12390.067-0.4831-0.07430.24570.16240.2777-0.2483-0.27840.1218-0.0359-0.02470.16050.03680.2172-19.9243-10.1558-16.1767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 215 )
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 234 )
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 245 )
7X-RAY DIFFRACTION7chain 'I' and (resid 1 through 7 )
8X-RAY DIFFRACTION8chain 'I' and (resid 8 through 15 )
9X-RAY DIFFRACTION9chain 'I' and (resid 16 through 32 )

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