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Yorodumi- PDB-8ep5: Solution NMR structure of a computationally designed mastoparan-l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ep5 | ||||||
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Title | Solution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R1 | ||||||
Components | Mastoparan-R1 peptide | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Antimicrobial Peptide / AMPs | ||||||
Function / homology | Function and homology information other organism cell membrane / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Vespula lewisii (insect) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Freitas, C.D.P. / Oshiro, K.G.N. / Macedo, M.L.R. / Cardoso, M.H. / Franco, O.L. / Liao, L.M. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Solution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R1. Authors: Freitas, C.D.P. / Oshiro, K.G.N. / Macedo, M.L.R. / Cardoso, M.H. / Franco, O.L. / Liao, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ep5.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ep5.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ep5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8ep5 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8ep5 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 1640.218 Da / Num. of mol.: 1 / Mutation: I1K, N2I, A5R, L9K, A10I / Source method: obtained synthetically / Source: (synth.) Vespula lewisii (insect) / References: UniProt: P01514 |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.5 mM Mastoparan-R1, 75 mM [U-98% 2H] SDS-d25, 0.05 % [U-98% 2H] DSS-d6, 90% H2O/10% D2O Label: Mastoparan-R1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: acid Not defined / Label: Mastoparan_R1 / pH: 4.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 5 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |