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- PDB-1t5m: Structural transitions as determinants of the action of the calci... -

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Basic information

Entry
Database: PDB / ID: 1t5m
TitleStructural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin
ComponentsDAPTOMYCIN
KeywordsANTIBIOTIC / DAPTOMYCIN / CUBICIN / LIPOPEPTIDE / CALCIUM-DEPENDENT
Function / homologyDaptomycin / DECANOIC ACID / :
Function and homology information
Biological speciesSTREPTOMYCES ROSEOSPORUS (bacteria)
MethodSOLUTION NMR
AuthorsJung, D. / Rozek, A. / Okon, M. / Hancock, R.E.
CitationJournal: Chem.Biol. / Year: 2004
Title: Structural Transitions as Determinants of the Action of the Calcium-Dependent Antibiotic Daptomycin.
Authors: Jung, D. / Rozek, A. / Okon, M. / Hancock, R.E.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Mar 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DAPTOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6572
Polymers1,4841
Non-polymers1721
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein/peptide DAPTOMYCIN / A21978C / CUBICIN


Type: Cyclic lipopeptide / Class: Antibiotic / Mass: 1484.440 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE ...Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION.
Source: (synth.) STREPTOMYCES ROSEOSPORUS (bacteria) / References: NOR: NOR00001, Daptomycin
#2: Chemical ChemComp-DKA / DECANOIC ACID


Type: Cyclic lipopeptide / Class: Antibiotic / Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE ...Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION.
References: Daptomycin
Compound detailsDAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER ...DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) DKA.
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
131DQF-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 2MM DAPTOMYCIN, 100MM KCL, 2MM EGTA, 0.2MM EDTA, 93% H2O, 7% D2O
Sample conditionsIonic strength: 100mM KCL / pH: 6.6 / Pressure: AMBIENT / Temperature: 290.15 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DGII MODULE OF INSIGHT II VER 97.2ACCYLRYS INC.refinement
DGII MODULE OF INSIGHT II VER 97.2structure solution
NMRPIPE 1structure solution
NMRVIEW 5.0.4structure solution
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 15

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