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- PDB-7bw5: a new lasso peptide koreensin -

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Basic information

Entry
Database: PDB / ID: 7bw5
Titlea new lasso peptide koreensin
Componentslasso peptide koreensin
KeywordsUNKNOWN FUNCTION / lasso peptide
Function / homologyBenenodin family lasso peptide
Function and homology information
Biological speciesSphingomonas koreensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHemmi, H. / Kodani, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K01913 Japan
CitationJournal: J Antibiot (Tokyo) / Year: 2021
Title: Heterologous production of new lasso peptide koreensin based on genome mining.
Authors: Fuwa, H. / Hemmi, H. / Kaweewan, I. / Kozaki, I. / Honda, H. / Kodani, S.
History
DepositionApr 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / 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 koreensin


Theoretical massNumber of molelcules
Total (without water)1,6731
Polymers1,6731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1630 Å2
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 koreensin


Mass: 1672.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas koreensis (bacteria) / Production host: Novosphingobium subterraneum (bacteria) / References: UniProt: A0A2M8WFL4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic21D 1H
121isotropic21D 13C
131isotropic2DEPT-135
141isotropic22D 1H-1H NOESY
151isotropic12D 1H-1H NOESY
161isotropic22D DQF-COSY
181isotropic22D 1H-1H TOCSY
171isotropic22D 1H-13C HSQC
191isotropic22D 1H-13C HMBC
1101isotropic22D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 3.0 mg/mL non labeled koreensin, DMSO / Label: non labeled / Solvent system: DMSO
SampleConc.: 3.0 mg/mL / Component: koreensin / Isotopic labeling: non labeled
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 0 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
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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