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- PDB-6j9p: Solution structure of a salt-resistant antimicrobial peptide, RR12 -

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Basic information

Entry
Database: PDB / ID: 6j9p
TitleSolution structure of a salt-resistant antimicrobial peptide, RR12
Componentssalt-resistant antimicrobial peptide RR12
KeywordsANTIMICROBIAL PROTEIN / AMP / SDS / Salt-resistant
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsTseng, T.S.
CitationJournal: To Be Published
Title: Solution structure of a salt-resistant antimicrobial peptide, RR12
Authors: Tseng, T.S.
History
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: 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: salt-resistant antimicrobial peptide RR12


Theoretical massNumber of molelcules
Total (without water)1,5961
Polymers1,5961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1640 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide salt-resistant antimicrobial peptide RR12


Mass: 1596.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic22D 1H-1H NOESY
151isotropic12D 1H-1H COSY
161isotropic22D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1.5 mg/mL RR12, 90% H2O/10% D2O / Label: natural / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mg/mL / Component: RR12 / Isotopic labeling: natural abundance
Sample conditionsIonic strength units: mM / Label: NA / pH: 5 / Pressure units: Pa / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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