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- PDB-2l2w: Thiostrepton -

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Basic information

Entry
Database: PDB / ID: 2l2w
TitleThiostrepton
ComponentsThiostrepton
KeywordsANTIBIOTIC / Natural antibiotic / Thiopeptide / Antimicrobial / ANTIBACTERIAL / thiazole / thiazoline
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / THIOSTREPTON / 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 1.3May 8, 2013Group: Derived calculations
Revision 2.0Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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

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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)1,8061
Polymers1,8061
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)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: 1805.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain ...Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes.
Source: (natural) Streptomyces azureus (bacteria) / References: UniProt: P0C8P8, THIOSTREPTON
Compound detailsTHIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC 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)
Has protein modificationY
Sequence detailsA MODIFIED QUINOLINE LINKED TO THE MAIN-CHAIN OF RESIDUE 1 AND THE SIDE-CHAIN OF RESIDUE 12.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Thiostrepton wt (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, chloroform-d/ethanol-d5 5:1 / Solvent system: chloroform-d/ethanol-d5 5:1
SampleConc.: 10 mM / Component: thiostrepton
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: 231 / NOE intraresidue total count: 76 / NOE long range total count: 55 / NOE sequential total count: 62
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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