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- PDB-5j6v: NMR structures of hylin-a1 analogs: Hylin-D -

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Basic information

Entry
Database: PDB / ID: 5j6v
TitleNMR structures of hylin-a1 analogs: Hylin-D
ComponentsHylin-D
KeywordsANTIMICROBIAL PROTEIN / Hylin-a1 analogues / antimicrobial peptides / DPC
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
AuthorsCrusca Jr., E. / Matos, C.O. / Liao, L.M. / Oliveira, A.L.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Sao Paulo Research Foundation (FAPESP) Brazil
FINEP-CTINFRA Brazil
CitationJournal: J. Pept. Sci. / Year: 2017
Title: NMR structures and molecular dynamics simulation of hylin-a1 peptide analogs interacting with micelles.
Authors: Crusca, E. / Camara, A.S. / Matos, C.O. / Marchetto, R. / Cilli, E.M. / Liao, L.M. / Lima de Oliveira, A.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Nov 13, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hylin-D


Theoretical massNumber of molelcules
Total (without water)2,0541
Polymers2,0541
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 / 200structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide Hylin-D


Mass: 2053.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hypsiboas albopunctatus (spotted treefrog) / References: UniProt: P85982
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-1H COSY

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Sample preparation

DetailsType: micelle / Contents: 100 mM [U-100% 2H] DPC-d38, 90% H2O/10% D2O / Label: Hylin-D / Solvent system: 90% H2O/10% D2O
SampleConc.: 100 mM / Component: DPC-d38 / Isotopic labeling: [U-100% 2H]
Sample conditionsDetails: 1 mM of Hylin-D / Ionic strength: PBS buffer Not defined / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 25 C

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
NMRViewstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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