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- PDB-2mn9: peptoid analogue of maculatin G15 - peptoid trans-Nleu at position 13 -

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Basic information

Entry
Database: PDB / ID: 2mn9
Titlepeptoid analogue of maculatin G15 - peptoid trans-Nleu at position 13
Componentsmaculatin G15
KeywordsANTIMICROBIAL PROTEIN / peptoid / N-substituted glycine / maculatin / antimicrobial peptide
Function / homologydefense response to bacterium / extracellular region / Maculatin-1.1
Function and homology information
Biological speciesLitoria genimaculata (brown-spotted treefrog)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model1
AuthorsUggerhoej, L.E. / Guentert, P. / Wimmer, R.
CitationJournal: Febs Lett. / Year: 2014
Title: Structural features of peptoid-peptide hybrids in lipid-water interfaces.
Authors: Uggerhj, L.E. / Munk, J.K. / Hansen, P.R. / Guntert, P. / Wimmer, R.
History
DepositionMar 29, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: maculatin G15


Theoretical massNumber of molelcules
Total (without water)2,1221
Polymers2,1221
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide maculatin G15 / Maculatin-1.1.1


Mass: 2121.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
Source: (synth.) Litoria genimaculata (brown-spotted treefrog)
References: UniProt: P82066*PLUS
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 COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 3 mM entity_1-1, 2 mM sodium azide-2, 150 mM [U-2H] SDS-3, 10 mM potassium phosphate-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMentity_1-11
2 mMsodium azide-21
150 mMSDS-3[U-2H]1
10 mMpotassium phosphate-41
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 310.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Shen, Cornilescu, Delaglio and Baxtorsion angle constraints from chemical shifts
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 155 / NOE intraresidue total count: 80 / NOE long range total count: 0 / NOE medium range total count: 24 / NOE sequential total count: 51 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 1 / Protein phi angle constraints total count: 16 / Protein psi angle constraints total count: 16
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.1 Å / Representative conformer: 1

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