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Entry
Database: PDB / ID: 2n0o
TitleNMR Solution Structure and Model Membrane Interaction Studies of the Peptide Hylin a1 from the Arboreal South American Frog Hypsiboas albopunctatus
ComponentsHylin-a1
KeywordsANTIMICROBIAL PROTEIN
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Hylin-a1
Function and homology information
Biological speciesHypsiboas albopunctatus (spotted treefrog)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model10
AuthorsAlves, E.S.F. / Oliveira, A.L.
CitationJournal: Protein Pept.Lett. / Year: 2015
Title: Micelle Bound Structure and Model Membrane Interaction Studies of the Peptide Hylin a1 from the Arboreal South American Frog Hypsiboas albopunctatus.
Authors: Alves, E.S. / Junior, E.C. / Cilli, E.M. / Castro, M.S. / Fontes, W. / de Magalhaes, M.T. / Liao, L.M. / de Oliveira, A.L.
History
DepositionMar 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hylin-a1


Theoretical massNumber of molelcules
Total (without water)1,8651
Polymers1,8651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Hylin-a1 / Hy-a1


Mass: 1865.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hypsiboas albopunctatus (spotted treefrog) / References: UniProt: P85982

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-1H COSY

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Sample preparation

DetailsContents: 1 mM Hylin a1, 100 mM [U-2H] SDS, 50 uM [U-99% 2H] D2O, 450 uM H2O, 1 mg/uL TMSP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHylin a1-11
100 mMSDS-2[U-2H]1
50 uMD2O-3[U-99% 2H]1
450 uMH2O-41
1 mg/mLTMSP-51
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clorestructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
ProcheckNMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 157 / NOE intraresidue total count: 60 / NOE long range total count: 22 / NOE medium range total count: 46 / NOE sequential total count: 51
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.5 Å / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.75 Å / Distance rms dev error: 0.24 Å

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