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- PDB-1xt7: Daptomycin NMR Structure -

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Basic information

Entry
Database: PDB / ID: 1xt7
TitleDaptomycin NMR Structure
ComponentsDAPTOMYCIN
KeywordsANTIBIOTIC / DAPTOMYCIN / CUBICIN / LIPOPEPTIDE / CALCIUM-DEPENDENT
Function / homologyDaptomycin / DECANOIC ACID / :
Function and homology information
Biological speciesSTREPTOMYCES ROSEOSPORUS (bacteria)
MethodSOLUTION NMR / CONSTRAINED MOLECULAR DYNAMICS
AuthorsBall, L.-J. / Goult, C.M. / Donarski, J.A. / Micklefield, J. / Ramesh, V.
CitationJournal: Org.Biomol.Chem. / Year: 2004
Title: NMR Structure Determination and Calcium Binding Effects of Lipopeptide Antibiotic Daptomycin
Authors: Ball, L.-J. / Goult, C.M. / Donarski, J.A. / Micklefield, J. / Ramesh, V.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 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)1 / -
Representative

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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 experimentType: 2D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
10.8MM DAPTOMYCIN
2PH 5.05
Sample conditionspH: 5.05 / Pressure: AMBIENT / Temperature: 298 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: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DYANA 1.5GUNTERT, P.refinement
XWINNMR 3.5structure solution
NMRPIPE 1.0structure solution
SPARKY 3.0structure solution
DYANA 1.5structure solution
RefinementMethod: CONSTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: A TOTAL OF 52 DISTANCE RESTRAINTS WERE USED FOR NMR STRUCTURE CALCULATION.
NMR ensembleConformers submitted total number: 1

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