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- PDB-6vl2: Stigmurin -

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Basic information

Entry
Database: PDB / ID: 6vl2
TitleStigmurin
ComponentsStigmurin
KeywordsANTIMICROBIAL PROTEIN / Scorpion venom / Antimicrobial Peptide / Amphipathic peptide / Non-disulfide-bridged peptide
Biological speciesTityus stigmurus (scorpion)
MethodSOLUTION NMR / simulated annealing
AuthorsRodrigues, S.C.S. / Resende, J.M. / Araujo, R.M. / Pedrosa, M.F.F.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
Citation
Journal: Peptides / Year: 2021
Title: NMR three-dimensional structure of the cationic peptide Stigmurin from Tityus stigmurus scorpion venom: In vitro antioxidant and in vivo antibacterial and healing activity.
Authors: Daniele-Silva, A. / Rodrigues, S.C.S. / Dos Santos, E.C.G. / Queiroz Neto, M.F. / Rocha, H.A.O. / Silva-Junior, A.A.D. / Resende, J.M. / Araujo, R.M. / Fernandes-Pedrosa, M.F.
#1: Journal: Peptides / Year: 2015
Title: Structural characterization of a novel peptide with antimicrobial activity from the venom gland of the scorpion Tityus stigmurus: Stigmurin.
Authors: de Melo, E.T. / Estrela, A.B. / Santos, E.C. / Machado, P.R. / Farias, K.J. / Torres, T.M. / Carvalho, E. / Lima, J.P. / Silva, A.A.J. / Barbosa, E.G. / Pedrosa, M.F.F.
History
DepositionJan 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stigmurin


Theoretical massNumber of molelcules
Total (without water)1,7951
Polymers1,7951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 Stigmurin


Mass: 1795.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: amidated C-terminal portion / Source: (synth.) Tityus stigmurus (scorpion)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H NOESY
121anisotropic12D 1H-1H TOCSY
131anisotropic12D 1H-15N HSQC
141anisotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 2.0 mM Stigmurin, 1.0 mM DSS, trifluoroethanol/water
Label: 2.0 nM / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMStigmurinnatural abundance1
1.0 mMDSSnatural abundance1
Sample conditionsDetails: 2.0 mM Stigmurin, 1.0 mM DSS, TFE-d2/H2O (40:60%, v/v)
Ionic strength: not applicable Not defined / Label: solution / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
TopSpinBruker Biospincollection
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOSCornilescu, Delaglio and Baxstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 14
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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