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- PDB-2mxh: NMR resolved structure of VG16KRKP, an antimicrobial peptide in SDS -

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Basic information

Entry
Database: PDB / ID: 2mxh
TitleNMR resolved structure of VG16KRKP, an antimicrobial peptide in SDS
Componentsantimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / turn / short helical segment
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsBhunia, A. / Datta, A.
CitationJournal: To be Published
Title: De-novo design of antimicrobial peptides:insights into membrane permeabilisation, lipopolysachharide fragmentation and application in plant disease control
Authors: Bhunia, A. / Datta, A.
History
DepositionJan 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
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: antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)1,7651
Polymers1,7651
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide antimicrobial peptide


Mass: 1765.157 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 0.5 mM antimicrobial peptide, 55.55 M H2O, 200 mM SDS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMantimicrobial peptide-11
55.55 MH2O-21
200 mMSDS-31
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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