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- PDB-2dcx: NMR solution structure of the Dermaseptin antimicrobial peptide a... -

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Basic information

Entry
Database: PDB / ID: 2dcx
TitleNMR solution structure of the Dermaseptin antimicrobial peptide analog NC12-K4S4(1-13)a
ComponentsDermaseptin-4
KeywordsANTIMICROBIAL PROTEIN / alpha-helix
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / 12-AMINO-DODECANOIC ACID / Dermaseptin-S4
Function and homology information
MethodSOLUTION NMR / Distance Geometry, Simulated Annealing
AuthorsShalev, D.E. / Rotem, S. / Fish, A. / Mor, A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Consequences of N-acylation on structure and membrane binding properties of dermaseptin derivative k4-s4-(1-13)
Authors: Shalev, D.E. / Rotem, S. / Fish, A. / Mor, A.
History
DepositionJan 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dermaseptin-4
A: 12-AMINO-DODECANOIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7292
Polymers1,5141
Non-polymers2151
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Dermaseptin-4 / DS IV


Mass: 1513.973 Da / Num. of mol.: 1 / Fragment: residues 1-13 / Mutation: M4K / Source method: obtained synthetically
Details: This is a truncated, mutated sequence of a peptide that occurs naturally in the South American tree frog, Phyllomedusa sauvagei.
References: UniProt: P80280
#2: Chemical ChemComp-DOA / 12-AMINO-DODECANOIC ACID


Type: L-peptide linking / Mass: 215.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H25NO2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY

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Sample preparation

DetailsContents: 2.2mM peptide; 20:1 molar ratio of DPC-d38 (Cambridge Isotope Laboratories, Inc., USA); 0.02% NaN3
Solvent system: 90% of 10% strength PBS solution, 10% D2O
Sample conditionsIonic strength: 78 mM / pH: 7.4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
XwinNMR3.1Brukerprocessing
Sparky3Goddard and Knellerdata analysis
X-PLOR3.856Nilges, Kuszewski and Brngerstructure solution
ProcheckLaskowski, Rullmannn, MacArthur, Kaptein and Thorntondata analysis
X-PLOR3.856Nilges, Kuszewski and Brngerrefinement
RefinementMethod: Distance Geometry, Simulated Annealing / Software ordinal: 1
Details: The structures are derived from 241 NOE constraints; 109 intraresidual; 44 i+1; 19 i+2; 39 i+3; 30 long-range.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 15

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