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Yorodumi- PDB-5u9v: Ocellatin-LB1, solution structure in DPC micelle by NMR spectroscopy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u9v | ||||||
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Title | Ocellatin-LB1, solution structure in DPC 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. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Ocellatin-LB1 Authors: Gusmao, K.A.G. / dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / 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 | 5u9v.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u9v.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 5u9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u9v_validation.pdf.gz | 355.6 KB | Display | wwPDB validaton report |
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Full document | 5u9v_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | 5u9v_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 5u9v_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/5u9v ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u9v | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 1.5 mM Ocellatin-LB1, 400 mM d38 DPC, 5 % 99.75% D2O, trifluoroethanol/water Label: Ocellatin-LB1-DPC / Solvent system: trifluoroethanol/water | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: Null / Label: Ocellatin-LB1 / pH: 4 / Pressure: ambient / Temperature: 273.15 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 | ||||||||||||||||||||||||||||||||||||||||
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 |