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- PDB-7mmm: LyeTx I -

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Basic information

Entry
Database: PDB / ID: 7mmm
TitleLyeTx I
ComponentsToxin LyeTx 1
KeywordsANTIMICROBIAL PROTEIN / Lycosa erythrognatha / Antimicrobial peptide / LyeTx / Spider venom.
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
AuthorsVerly, R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Minas Gerais State Agency for Research and Development (FAPEMIG) Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Amino Acids / Year: 2010
Title: LyeTx I, a potent antimicrobial peptide from the venom of the spider Lycosa erythrognatha
Authors: Verly, R.M. / Lima, M.E.
History
DepositionApr 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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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)2,8381
Polymers2,8381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Toxin LyeTx 1


Mass: 2837.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lycosa erythrognatha (spider) / References: UniProt: C0HJU9
Has ligand of interestN
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 HSQC

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Sample preparation

DetailsType: solution / Contents: 2 mM LyeTx I, 95% H2O/5% D2O / Label: LyeTx I - DPC / Solvent system: 95% H2O/5% D2O
SampleConc.: 2 mM / Component: LyeTx I / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 20 mM / Label: LyeTx I - DPC / pH: 7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz
Details: triple-resonance (1H/13C/15N) gradient probe (5 mm diameter)]

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
QUEENNabuurs, Spronk, Krieger, Maassen, Vriend and Vuisterdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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