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- PDB-2mw3: Solution NMR structure of the lasso peptide streptomonomicin -

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Basic information

Entry
Database: PDB / ID: 2mw3
TitleSolution NMR structure of the lasso peptide streptomonomicin
ComponentsLasso peptide
KeywordsUNKNOWN FUNCTION / lasso peptide / antibiotic / macrocycle / RiPP
Function / homologyStreptomonomicin peptide protein
Function and homology information
Biological speciesStreptomonospora alba (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTietz, J.I. / Zhu, L. / Mitchell, D.A. / Metelev, M. / Melby, J.O. / Blair, P.M. / Livnat, I. / Severinov, K.
CitationJournal: Chem.Biol. / Year: 2015
Title: Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso Peptide from an understudied halophilic actinomycete.
Authors: Metelev, M. / Tietz, J.I. / Melby, J.O. / Blair, P.M. / Zhu, L. / Livnat, I. / Severinov, K. / Mitchell, D.A.
History
DepositionOct 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lasso peptide


Theoretical massNumber of molelcules
Total (without water)2,2531
Polymers2,2531
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)15 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Lasso peptide


Mass: 2252.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomonospora alba (bacteria) / References: UniProt: A0A0C2JEQ8*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-13C HSQC
1512D 1H-13C HMBC

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Sample preparation

DetailsContents: 4 mM streptomonomicin, 100% methanol / Solvent system: 100% methanol
SampleConc.: 4 mM / Component: streptomonomicin-1
Sample conditionsTemperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.36C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clorestructure solution
X-PLOR NIH2.36C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clorerefinement
Sparky3.115Goddardpeak picking
NMRPipe8.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJ3.2AVariancollection
MestReNova8.1.1Mestrelabchemical shift assignment
MestReNova8.1.1Mestrelabprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 328 / NOE intraresidue total count: 137 / NOE long range total count: 79 / NOE medium range total count: 30 / NOE sequential total count: 82
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 15

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