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- PDB-1xkm: NMR structure of antimicrobial peptide distinctin in water -

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Basic information

Entry
Database: PDB / ID: 1xkm
TitleNMR structure of antimicrobial peptide distinctin in water
Components
  • Distinctin chain A
  • Distinctin chain B
KeywordsANTIBIOTIC / PORE-FORMING PEPTIDE / HETERODIMER / HOMODIMER / DISULFIDE / FOUR-HELIX BUNDLE
MethodSOLUTION NMR / simulated annealing with cartesian coordinate dynamics
AuthorsAmodeo, P. / Raimondo, D. / Andreotti, G. / Motta, A. / Scaloni, A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A folding-dependent mechanism of antimicrobial peptide resistance to degradation unveiled by solution structure of distinctin.
Authors: Raimondo, D. / Andreotti, G. / Saint, N. / Amodeo, P. / Renzone, G. / Sanseverino, M. / Zocchi, I. / Molle, G. / Motta, A. / Scaloni, A.
#1: Journal: Febs Lett. / Year: 2001
Title: A novel heterodimeric antimicrobial peptide from the tree-frog Phyllomedusa distincta
Authors: Batista, C.V. / Scaloni, A. / Rigden, D.J. / Silva, L.R. / Rodrigues Romero, A. / Dukor, R. / Sebben, A. / Talamo, F. / Bloch, C.
History
DepositionSep 29, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Distinctin chain A
B: Distinctin chain B
C: Distinctin chain A
D: Distinctin chain B


Theoretical massNumber of molelcules
Total (without water)10,9854
Polymers10,9854
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)24 / 150Structures within a prefixed threshold of amber energy, solvent accessible surface area and symmetry-based penalty functions (see jrnl)
RepresentativeModel #20structure within a prefixed threshold of amber energy, solvent accessible surface area and symmetry-based penalty functions

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Components

#1: Protein/peptide Distinctin chain A


Mass: 2532.076 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was prepared by solid-phase synthesis. This sequence occurs naturally in the tree-frog Phyllomedusa distincta
#2: Protein/peptide Distinctin chain B


Mass: 2960.563 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was prepared by solid-phase synthesis. This sequence occurs naturally in the tree-frog Phyllomedusa distincta
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
2312D NOESY
2412D TOCSY
1522D NOESY
1622D TOCSY
2722D NOESY
2822D TOCSY
3932D NOESY
31032D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.8mM Natural Abundance Distinctin; NaN390% H2O/10% D2O
20.05mM Natural Abundance Distinctin; NaN390% H2O/10% D2O
33.8mM Natural Abundance Distinctin; NaN3100% D2O
40.05mM Natural Abundance Distinctin; NaN3100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1NULL 6.8ambient 310 K
2NULL 6.8ambient 300 K
3NULL 6.4ambient 310 K
4NULL 6.4ambient 300 K
5NULL 5.4ambient 310 K
6NULL 5.4ambient 300 K
7NULL 5ambient 310 K
8NULL 5ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber5Kollman, Casestructure solution
Amber5Kollman, Caserefinement
MOLMOL2K.2Koradidata analysis
XwinNMR2Brukerprocessing
RefinementMethod: simulated annealing with cartesian coordinate dynamics
Software ordinal: 1
Details: the structures are based on a total of 636 restraints, 548 are NOE-derived distance constraints, 88 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: structure within a prefixed threshold of amber energy, solvent accessible surface area and symmetry-based penalty functions
NMR ensembleConformer selection criteria: Structures within a prefixed threshold of amber energy, solvent accessible surface area and symmetry-based penalty functions (see jrnl)
Conformers calculated total number: 150 / Conformers submitted total number: 24

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