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Yorodumi- PDB-5ua6: Ocellatin-LB1, solution structure in SDS micelle by NMR spectroscopy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ua6 | ||||||
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Title | Ocellatin-LB1, solution structure in SDS micelle by NMR spectroscopy | ||||||
Components | Ocellatin-LB1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / OCELLATIN / ANTIMICROBIAL PEPTIDE / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION | ||||||
Function / homology | Ocellatin / Ocellatin family / hemolysis by symbiont of host erythrocytes / defense response to fungus / defense response to bacterium / extracellular region / Ocellatin-LB1 Function and homology information | ||||||
Biological species | Leptodactylus labyrinthicus (frog) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Gusmao, K.A.G. / dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / de Lima, M.E. / Resende, J.M. | ||||||
Citation | Journal: Peptides / Year: 2018 Title: NMR structures in different membrane environments of three ocellatin peptides isolated from Leptodactylus labyrinthicus. Authors: Gomes, K.A.G.G. / Dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / Mundim, H.M. / Rodrigues, L.V. / Liao, L.M. / Verly, R.M. / de Lima, M.E. / Resende, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ua6.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ua6.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ua6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ua6_validation.pdf.gz | 365.7 KB | Display | wwPDB validaton report |
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Full document | 5ua6_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 5ua6_validation.xml.gz | 7 KB | Display | |
Data in CIF | 5ua6_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/5ua6 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/5ua6 | HTTPS FTP |
-Related structure data
Related structure data | 5u9qC 5u9rC 5u9yC 5ua7C 5ua8C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2195.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptodactylus labyrinthicus (frog) / References: UniProt: C0HKF1*PLUS |
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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 Ocellatin-LB1, 1 mM DSS, 400 mM d-25 SDS, 5 % 99.75 D2O, 95% H2O/5% D2O Label: Ocellatin-LB1-SDS / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: Null / Label: ocellatin-LB1 / pH: 4 / Pressure: Ambient / Temperature: 303.15 K |
-NMR measurement
NMR spectrometer | Type: Bruker AvanceIII / Manufacturer: Bruker / Model: AvanceIII / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 7 / Details: X-PLOR NIH | ||||||||||||||||||||||||||||||
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 |