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- PDB-6a5j: solution NMR Structure of small peptide -

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Basic information

Entry
Database: PDB / ID: 6a5j
Titlesolution NMR Structure of small peptide
ComponentsILE-LYS-LYS-ILE-LEU-SER-LYS-ILE-LYS-LYS-LEU-LEU-LYS
KeywordsANTIMICROBIAL PROTEIN / anticancer / antibiotic
Biological speciesRana chensinensis (Chinese brown frog)
MethodSOLUTION NMR / simulated annealing
AuthorsFeng, L.B. / Dong, W.B.
CitationJournal: To Be Published
Title: The solution NMR Structure of antimicrobial peptide L-K6, the analog of temporin-1CEB derived from the skin secretions of Chinese brown frog Rana chensinenesis
Authors: Feng, L.B. / Dong, W.B.
History
DepositionJun 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ILE-LYS-LYS-ILE-LEU-SER-LYS-ILE-LYS-LYS-LEU-LEU-LYS


Theoretical massNumber of molelcules
Total (without water)1,5591
Polymers1,5591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ILE-LYS-LYS-ILE-LEU-SER-LYS-ILE-LYS-LYS-LEU-LEU-LYS / Chinese brown frog


Mass: 1559.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rana chensinensis (Chinese brown frog)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 3 mM LK6, 90% H2O/TFE(6:4 v/v), 10% D2O / Label: peptide_sample / Solvent system: 90% H2O/TFE(6:4 v/v), 10% D2O
SampleConc.: 3 mM / Component: LK6 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: c1 / pH: 4.5 / Pressure: ambient bar / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS/Aria2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 100 / Conformers submitted total number: 20

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