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- PDB-2l2y: Thiostrepton, epimer form of residue 9 -

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Basic information

Entry
Database: PDB / ID: 2l2y
TitleThiostrepton, epimer form of residue 9
ComponentsThiostrepton
KeywordsANTIBIOTIC / Natural antibiotic / Thiopeptide / Antimicrobial / ANTIBACTERIAL / thiazole / thiazoline
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / THIOPEPTIDE THIOSTREPTON WITH EPIMER FORM OF RESIDUE 9 / Thiostrepton
Function and homology information
Biological speciesStreptomyces azureus (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsJonker, H.R.A. / Baumann, S. / Wolf, A. / Schoof, S. / Hiller, F. / Schulte, K.W. / Kirschner, K.N. / Schwalbe, H. / Arndt, H.-D.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: NMR structures of thiostrepton derivatives for characterization of the ribosomal binding site.
Authors: Jonker, H.R. / Baumann, S. / Wolf, A. / Schoof, S. / Hiller, F. / Schulte, K.W. / Kirschner, K.N. / Schwalbe, H. / Arndt, H.D.
History
DepositionAug 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Jun 26, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiostrepton


Theoretical massNumber of molelcules
Total (without water)1,7371
Polymers1,7371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Thiostrepton / / Alaninamide / Bryamycin / Gargon / Thiactin


Type: Thiopeptide / Class: Antibiotic / Mass: 1736.923 Da / Num. of mol.: 1 / Fragment: residues 1-16 / Mutation: (DCY)9C / Source method: isolated from a natural source
Details: THIOSTREPTON IS A HETEROCYCLIC THIOPEPTIDE, CONSISTING OF FOUR THIAZOLES ONE THIOZOLINE ONE PIPERIDEINE RINGS. A MODIFIED QUINOLINE, RESIDUE 0, IS LINKED TO MAIN-CHAIN RESIDUE 1 AND SIDE- ...Details: THIOSTREPTON IS A HETEROCYCLIC THIOPEPTIDE, CONSISTING OF FOUR THIAZOLES ONE THIOZOLINE ONE PIPERIDEINE RINGS. A MODIFIED QUINOLINE, RESIDUE 0, IS LINKED TO MAIN-CHAIN RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12. IN THIS ENTRY RESIDUE 9 WAS CHEMICALLY MODIFIED FROM D-CYS TO L-CYS AND RESIDUE 17 (HET DHA) WAS DELETED.
Source: (natural) Streptomyces azureus (bacteria)
References: UniProt: P0C8P8, THIOPEPTIDE THIOSTREPTON WITH EPIMER FORM OF RESIDUE 9
Compound detailsTHIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYCLIC ...THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYCLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES)
Sequence detailsA MODIFIED QUINOLINE LINKED TO THE MAIN-CHAIN OF RESIDUE 1 AND THE SIDE-CHAIN OF RESIDUE 12. THE ...A MODIFIED QUINOLINE LINKED TO THE MAIN-CHAIN OF RESIDUE 1 AND THE SIDE-CHAIN OF RESIDUE 12. THE RESIDUE 9 HAS BEEN MODIFIED TO CYS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Thiostrepton derivative (epimer form of residue thc9:c5, in 5:1 chloroform-d ethanol-d5)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C TOCSY-HSQC
1412D 1H-13C HMBC
1512D 1H-1H NOESY
1612D 1H-1H ROESY
1712D 1H-1H TOCSY

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Sample preparation

DetailsContents: 10 mM thiostrepton (epi,9), chloroform-d/ethanol-d5 5:1
Solvent system: chloroform-d/ethanol-d5 5:1
SampleConc.: 10 mM / Component: thiostrepton (epi,9)
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPIN1.3Bruker Biospincollection
TOPSPIN1.3Bruker Biospinprocessing
SPARKY3.113Goddardpeak picking
SPARKY3.113Goddardchemical shift assignment
SPARKY3.113Goddarddata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 170 / NOE intraresidue total count: 68 / NOE long range total count: 42 / NOE sequential total count: 47
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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