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- PDB-5u9y: Ocellatin-F1 -

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Basic information

Entry
Database: PDB / ID: 5u9y
TitleOcellatin-F1
ComponentsOcellatin-K1
KeywordsANTIMICROBIAL PROTEIN / OCELLATIN / ANTIMICROBIAL PEPTIDE / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION
Function / homologyOcellatin / Ocellatin family / hemolysis by symbiont of host erythrocytes / defense response to bacterium / extracellular region / Ocellatin-K1
Function and homology information
Biological speciesLeptodactylus knudseni (Knudsen's thin-toed 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.
CitationJournal: 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
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_number_of_molecules
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 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-K1


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-K1


Mass: 2552.089 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Leptodactylus knudseni (Knudsen's thin-toed frog)
References: UniProt: P86711
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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 2 mM Ocellatin-F1, 400 mM d-38 DPC, 5 % 99.75 D2O, 1 mM DSS, 95% H2O/5% D2O
Label: Ocellatin-F1-DPC / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMOcellatin-F1natural abundance1
400 mMDPCd-381
5 %D2O99.751
1 mMDSSnatural abundance1
Sample conditionsIonic strength: Null / Label: Ocellatin-F1 / pH: 4 / Pressure: Ambient / Temperature: 293.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 7
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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