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- PDB-2jx6: Structure and membrane interactions of the antibiotic peptide der... -

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Entry
Database: PDB / ID: 2jx6
TitleStructure and membrane interactions of the antibiotic peptide dermadistinctin k by solution and oriented 15N and 31P solid-state NMR spectroscopy
ComponentsDermadistinctin-K
KeywordsANTIMICROBIAL PROTEIN / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION / MEMBRANE PEPTIDE / Amphibian defense peptide / Antibiotic / Antimicrobial / Secreted
Function / homologyDermaseptin / Dermaseptin / defense response to bacterium / extracellular region / Dermaseptin-DI1
Function and homology information
Biological speciesPhyllomedusa distincta (Sao Paulo leaf frog)
MethodSOLUTION NMR / simulated annealing
AuthorsMendonca Moraes, C. / Verly, R.M. / Resende, J.M. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A. / Almeida, F.C.L. / Bechinger, B.
CitationJournal: Biophys.J. / Year: 2009
Title: Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy
Authors: Verly, R.M. / de Moraes, C.M. / Resende, J.M. / Aisenbrey, C. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A.P. / Almeida, F.C.L. / Bechinger, B.
History
DepositionNov 8, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Assembly

Deposited unit
A: Dermadistinctin-K


Theoretical massNumber of molelcules
Total (without water)3,1571
Polymers3,1571
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)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Dermadistinctin-K / DD K


Mass: 3156.699 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was synthesized by solid-phase synthesis using fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of phyllomedusa distincta, ...Details: The peptide was synthesized by solid-phase synthesis using fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of phyllomedusa distincta, a frog species found in brazilian forests.
Source: (synth.) Phyllomedusa distincta (Sao Paulo leaf frog)
References: UniProt: P83638
Has protein modificationY

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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-13C HSQC
1412D 1H-15N HSQC

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Sample preparation

DetailsContents: 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40%
Solvent system: trifluoroethanol; H2O 60%, D2O 40%
SampleConc.: 2.0 mM / Component: dermadistinctin k
Sample conditionspH: 7 / Pressure: ambient / Temperature: 293.15 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thdata analysis
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, ...Details: NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, respectively). Structure calculations were performed using the Xplor-NIH software, version 2.17.0 . Starting with the extended structure, 500 structures were generated using a simulated annealing protocol. This was followed by 20000 steps of simulated annealing at 1000 K and a subsequent decrease in tempera ure in 15000 steps in the first slow-cool annealing stage.
NMR constraintsNOE constraints total: 294 / NOE intraresidue total count: 178 / NOE long range total count: 0 / NOE medium range total count: 38 / NOE sequential total count: 78
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 19

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