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Basic information

Entry
Database: PDB / ID: 5cy0
TitleTotal Chemical Synthesis, Covalent Structure Verification, and X-ray Structure of Bioactive Ts3 Toxin by Racemic Protein Crystallography
ComponentsTs3 Toxin
KeywordsTOXIN / Racemic Structure / Nav ligand / central symmetric
Function / homology
Function and homology information


sodium channel inhibitor activity / : / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-mammal toxin Ts3
Similarity search - Component
Biological speciesTityus serrulatus (Brazilian scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDang, B. / Kubota, T. / Mandal, K. / Correa, A.M. / Bezanilla, F. / Kent, S.B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01- GM030376 United States
American Heart Association13POST14800031 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin.
Authors: Dang, B. / Kubota, T. / Mandal, K. / Correa, A.M. / Bezanilla, F. / Kent, S.B.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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: Ts3 Toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7424
Polymers7,4651
Non-polymers2763
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-1 kcal/mol
Surface area4420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)19.322, 30.406, 52.468
Angle α, β, γ (deg.)101.17, 91.26, 98.61
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein Ts3 Toxin / Tityustoxin V / TsV / Toxin V / Toxin-5


Mass: 7465.436 Da / Num. of mol.: 1 / Fragment: UNP residues 14-77 / Source method: obtained synthetically / Source: (synth.) Tityus serrulatus (Brazilian scorpion) / References: UniProt: P01496
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: BIS-TRIS, Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→18.2 Å / Num. obs: 9391 / % possible obs: 92 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.242 / Net I/σ(I): 4.4
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ASC

2asc


Resolution: 1.93→18.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3043 382 4.81 %
Rwork0.2564 --
obs0.2587 7934 91.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→18.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 18 67 583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007546
X-RAY DIFFRACTIONf_angle_d0.936732
X-RAY DIFFRACTIONf_dihedral_angle_d12.032193
X-RAY DIFFRACTIONf_chiral_restr0.03568
X-RAY DIFFRACTIONf_plane_restr0.00590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.20890.4121300.35342461X-RAY DIFFRACTION90
2.2089-2.78130.31571230.31722540X-RAY DIFFRACTION91
2.7813-18.20090.27241290.20792551X-RAY DIFFRACTION93
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)
17.26850.45521.63024.05213.73696.43730.00760.3587-0.46950.13650.1582-0.00120.04830.3838-0.05220.13630.01720.01070.1440.00630.17492.44493.281212.7705
21.09980.40060.01347.89144.54174.713-0.21410.52780.6185-1.01150.06410.121-1.1962-0.0281-0.0030.4377-0.0175-0.0730.19020.10750.28570.967711.29398.4161
36.1282-0.7825-1.12117.07193.55758.0158-0.16520.49320.5883-0.54940.3972-0.1037-0.90440.4208-0.24420.23-0.0652-0.02750.23850.02040.23325.643210.505212.1363
45.5477-2.4898-4.02694.53582.08934.57150.0090.5262-0.1787-0.1292-0.03140.1316-0.14470.4431-0.03870.1482-0.0072-0.04280.3233-0.03080.15459.55583.33279.7988
54.11820.4676-0.95368.45632.86775.6942-0.1225-0.5526-0.68360.37570.2588-0.29380.8930.3177-0.14790.29150.0623-0.0130.22030.01140.33913.32313.028921.6057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 48 )
5X-RAY DIFFRACTION5chain 'A' and (resid 49 through 63 )

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