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Yorodumi- PDB-6cl3: LyeTxI-b, a synthetic peptide derived from Lycosa erythrognatha s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cl3 | ||||||
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Title | LyeTxI-b, a synthetic peptide derived from Lycosa erythrognatha spider venom, shows potent antibiotic activity, in vitro and in vivo | ||||||
Components | Toxin LyeTx 1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antimicrobial peptide | ||||||
Function / homology | hemolysis in another organism / toxin activity / defense response to bacterium / extracellular region / Toxin LyeTx 1 Function and homology information | ||||||
Biological species | Lycosa erythrognatha (spider) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | de Lima, M.E. / dos Reis, P.V. / Resende, J.M. / Verly, R.M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cl3.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cl3.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 6cl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/6cl3 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/6cl3 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2725.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lycosa erythrognatha (spider) / References: UniProt: C0HJU9 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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) | ||||||||||||||||
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Sample |
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Sample conditions | Details: 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: 7.0 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance III 600 / Manufacturer: Bruker / Model: Avance III 600 / Field strength: 600.043 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |