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Yorodumi- PDB-6g4u: The solution NMR structure of brevinin-1BYa in dodecylphosphochol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g4u | ||||||
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Title | The solution NMR structure of brevinin-1BYa in dodecylphosphocholine micelles | ||||||
Components | Brevinin-1BYa | ||||||
Keywords | ANTIMICROBIAL PROTEIN / cationic / rana-box / antimicrobial peptide | ||||||
Function / homology | Frog antimicrobial peptide, brevinin-1 type / Frog antimicrobial peptide / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Brevinin-1BYa Function and homology information | ||||||
Biological species | Rana boylii (yellow-legged frog) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Timmons, P.B. / O'Flynn, D.P. / Conlon, J.M. / Hewage, C.M. | ||||||
Citation | Journal: J.Pept.Sci. / Year: 2019 Title: Structural and positional studies of the antimicrobial peptide brevinin-1BYa in membrane-mimetic environments. Authors: Timmons, P.B. / O'Flynn, D. / Conlon, J.M. / Hewage, C.M. #1: Journal: J. Pept. Res. / Year: 2003 Title: Isolation of peptides of the brevinin-1 family with potent candidacidal activity from the skin secretions of the frog Rana boylii. Authors: Conlon, J.M. / Sonnevend, A. / Patel, M. / Davidson, C. / Nielsen, P.F. / Pal, T. / Rollins-Smith, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g4u.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g4u.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g4u_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 6g4u_full_validation.pdf.gz | 741 KB | Display | |
Data in XML | 6g4u_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 6g4u_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g4u ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g4u | HTTPS FTP |
-Related structure data
Related structure data | 6g4iC 6g4kC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: 2613.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rana boylii (yellow-legged frog) / References: UniProt: P84111 |
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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: 1.5 mM NA- brevinin-1BYa, 280 mM [U-99% 2H] DPC, 90% H2O/10% D2O Label: sample_1 / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 Not defined / Label: conditions_1 / pH: 7 / Pressure: 100000 Pa / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: medoid | |||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |