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- PDB-6cl3: LyeTxI-b, a synthetic peptide derived from Lycosa erythrognatha s... -

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Basic information

Entry
Database: PDB / ID: 6cl3
TitleLyeTxI-b, a synthetic peptide derived from Lycosa erythrognatha spider venom, shows potent antibiotic activity, in vitro and in vivo
ComponentsToxin LyeTx 1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homologytoxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / Toxin LyeTx 1
Function and homology information
Biological speciesLycosa erythrognatha (spider)
MethodSOLUTION NMR / simulated annealing
Authorsde Lima, M.E. / dos Reis, P.V. / Resende, J.M. / Verly, R.M.
CitationJournal: Front Microbiol / Year: 2018
Title: LyeTxI-b, a Synthetic Peptide Derived FromLycosa erythrognathaSpider Venom, Shows Potent Antibiotic Activityin Vitroandin Vivo.
Authors: Reis, P.V.M. / Boff, D. / Verly, R.M. / Melo-Braga, M.N. / Cortes, M.E. / Santos, D.M. / Pimenta, A.M.C. / Amaral, F.A. / Resende, J.M. / de Lima, M.E.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin LyeTx 1


Theoretical massNumber of molelcules
Total (without water)2,7251
Polymers2,7251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint0 kcal/mol
Surface area2530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Toxin LyeTx 1


Mass: 2725.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lycosa erythrognatha (spider) / References: UniProt: C0HJU9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HMQC

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Sample preparation

DetailsType: solution
Contents: 2 mM LyeTxI-b, 20 mM phosphate buffer, 1 mM DSS, TFE-d2/H2O (60:40%, v/v)
Label: None / Solvent system: TFE-d2/H2O (60:40%, v/v)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMLyeTxI-bnatural abundance1
20 mMphosphate buffernatural abundance1
1 mMDSSnatural abundance1
Sample conditionsDetails: 2.0 mM peptide at TFE-d2/H2O (60:40%, v/v), pH pH 7.0 (20 mM phosphate buffer) 1.0 mM DSS (internal reference)
Ionic strength: not applicable Not defined / Label: TFE-d2:H2O / pH: 7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance III 600 / Manufacturer: Bruker / Model: Avance III 600 / Field strength: 600.043 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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