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- PDB-6fgm: The NMR solution structure of the peptide AC12 from Hypsiboas raniceps -

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Basic information

Entry
Database: PDB / ID: 6fgm
TitleThe NMR solution structure of the peptide AC12 from Hypsiboas raniceps
ComponentsALA-CYS-PHE-LEU-THR-ARG-LEU-GLY-THR-TYR-VAL-CYS
KeywordsIMMUNE SYSTEM / AC12 peptide
Biological speciesHypsiboas raniceps (Chaco treefrog)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPopov, C.S.F.C. / Simas, B.S. / Goodfellow, B.J. / Bocca, A.L. / Andrade, P.B. / Pereira, D. / Valentao, P. / Pereira, P.J.B. / Rodrigues, J.E. / Veloso Jr, P.H.H. / Rezende, T.M.B.
Funding support Brazil, Portugal, 5items
OrganizationGrant numberCountry
CAPES Brazil
CNPq Brazil
FAP-DF Brazil
FCT/MEC Portugal
FEDER Portugal
CitationJournal: Peptides / Year: 2019
Title: Host-defense peptides AC12, DK16 and RC11 with immunomodulatory activity isolated from Hypsiboas raniceps skin secretion.
Authors: Popov, C.S.F.C. / Magalhaes, B.S. / Goodfellow, B.J. / Bocca, A.L. / Pereira, D.M. / Andrade, P.B. / Valentao, P. / Pereira, P.J.B. / Rodrigues, J.E. / de Holanda Veloso Junior., P.H. / Rezende, T.M.B.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
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
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4May 5, 2021Group: Data collection / Structure summary / Category: audit_author / pdbx_nmr_spectrometer / Item: _audit_author.name / _pdbx_nmr_spectrometer.model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALA-CYS-PHE-LEU-THR-ARG-LEU-GLY-THR-TYR-VAL-CYS


Theoretical massNumber of molelcules
Total (without water)1,3481
Polymers1,3481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ALA-CYS-PHE-LEU-THR-ARG-LEU-GLY-THR-TYR-VAL-CYS


Mass: 1347.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Disulfide bond 2-12 / Source: (natural) Hypsiboas raniceps (Chaco treefrog)

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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-1H ROESY

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Sample preparation

DetailsType: solution / Contents: 1.0 mM NA ac12, 93% H2O/7% D2O / Label: H2O / Solvent system: 93% H2O/7% D2O
SampleConc.: 1.0 mM / Component: ac12 / Isotopic labeling: NA
Sample conditionsIonic strength: NA Not defined / Label: conditions_1 / pH: 4.0 pH* / PH err: 0.05 / Pressure: AMBIENT atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Pstructure calculation
TopSpin3Bruker Biospincollection
SparkyNMRFAM-SPARKY 1.412Goddard TD & Kneller DG (2008) SPARKY 3. University of California, San Francisco. Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.peak picking
TopSpin3Bruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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