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- PDB-6iha: antibacterial peptide SibaCec-A -

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Basic information

Entry
Database: PDB / ID: 6iha
Titleantibacterial peptide SibaCec-A
ComponentsSibaCec-A
KeywordsANTITOXIN / antibacterial peptide / alpha-helix
Function / homologyCecropin 4
Function and homology information
Biological speciesSimulium bannaense (insect)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsJing, H. / Lin, W.
CitationJournal: To Be Published
Title: antibacterial peptide SibaCec-A
Authors: Jing, H. / Lin, W.
History
DepositionSep 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SibaCec-A


Theoretical massNumber of molelcules
Total (without water)3,1151
Polymers3,1151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2860 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide SibaCec-A


Mass: 3114.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Simulium bannaense (insect) / References: UniProt: A0A0U2QEK1*PLUS

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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 DQF-COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 3.0 mM peptide, trifluoroethanol/water / Label: sample / Solvent system: trifluoroethanol/water
SampleConc.: 3.0 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: TFE / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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