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- PDB-5u9s: Ocellatin-F1, solution structure in TFE by NMR spectroscopy -

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Basic information

Entry
Database: PDB / ID: 5u9s
TitleOcellatin-F1, solution structure in TFE by NMR spectroscopy
ComponentsOcellatin-F1
KeywordsANTIMICROBIAL PROTEIN / OCELLATIN / ANTIMICROBIAL PEPTIDE / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION
Function / homologyOcellatin / Ocellatin family / hemolysis by symbiont of host erythrocytes / regulation of defense response to virus / defense response to fungus / defense response to bacterium / extracellular region / Ocellatin-F1
Function and homology information
Biological speciesLeptodactylus labyrinthicus (frog)
MethodSOLUTION NMR / simulated annealing
AuthorsGusmao, K.A.G. / dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / de Lima, M.E. / Resende, J.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
CAPES Brazil
CitationJournal: To Be Published
Title: Ocellatin-F1
Authors: Gusmao, K.A.G. / dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / de Lima, M.E. / Resende, J.M.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ocellatin-F1


Theoretical massNumber of molelcules
Total (without water)2,5521
Polymers2,5521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Ocellatin-F1


Mass: 2552.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptodactylus labyrinthicus (frog) / References: UniProt: C0HKF0*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 2.0 mM Ocellatin-F1, 1.0 mM DSS, 20 mM potassium phosphate, 60 % d2 TFE, 40 % H2O, trifluoroethanol/water
Details: ph 7, potassium phosphate bufer / Label: Ocellati-F1-TFE / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMOcellatin-F1natural abundance1
1.0 mMDSSnatural abundance1
20 mMpotassium phosphatenatural abundance1
60 %TFEd21
40 %H2Onatural abundance1
Sample conditionsIonic strength: null Not defined / Label: Ocellatin-F1-TFE / pH: 7 / Pressure: Ambient / Temperature: 293.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMRBruker Biospincollection
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
X-PLOR NIH2.27Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.27Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH2.27Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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