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Yorodumi- PDB-8b1l: NMR structure of the antimicrobial peptide Of-Pis1 in DPC micelles -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b1l | ||||||
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Title | NMR structure of the antimicrobial peptide Of-Pis1 in DPC micelles | ||||||
Components | Piscidin | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Piscidin / histidine-rich peptide / membrane interaction | ||||||
Function / homology | Pleurocidin / Pleurocidin family / defense response to bacterium / Piscidin Function and homology information | ||||||
Biological species | Oplegnathus fasciatus (barred knifejaw) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Alaimo, N. / Bischetti, M. / Gallo, M. / Cicero, D.O. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Biochim Biophys Acta Biomembr / Year: 2022 Title: Structural insights on the selective interaction of the histidine-rich piscidin antimicrobial peptide Of-Pis1 with membranes. Authors: Bischetti, M. / Alaimo, N. / Nardelli, F. / Punzi, P. / Amariei, C. / Ingenito, R. / Musco, G. / Gallo, M. / Cicero, D.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b1l.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b1l.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 8b1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b1l_validation.pdf.gz | 340 KB | Display | wwPDB validaton report |
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Full document | 8b1l_full_validation.pdf.gz | 363.2 KB | Display | |
Data in XML | 8b1l_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 8b1l_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/8b1l ftp://data.pdbj.org/pub/pdb/validation_reports/b1/8b1l | HTTPS FTP |
-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: 2583.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oplegnathus fasciatus (barred knifejaw) / References: UniProt: M5AE98 |
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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: micelle Contents: 3 mM Of-Pis1, 60 mM [U-2H] DPC, 20 mM sodium phosphate, 90% H2O/10% D2O Label: DPC_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 40 mM / Label: cond_1 / pH: 5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 Details: the structures are based on a total of 453 NOE-derived distances constraints and 17 dihedral angles restraints | |||||||||||||||||||||
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: 20 |