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- PDB-5zcn: Solution NMR structure of a new lasso peptide brevunsin -

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Basic information

Entry
Database: PDB / ID: 5zcn
TitleSolution NMR structure of a new lasso peptide brevunsin
Componentsbrevunsin
KeywordsUNKNOWN FUNCTION / lasso peptide / Sphingomonas subterranea / brevunsin
Function / homologyUncharacterized protein / :
Function and homology information
Biological speciesBrevundimonas diminuta (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHemmi, H. / Kodani, S. / Miyake, Y. / Kaweewan, I. / Nakagawa, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25350964 Japan
CitationJournal: J. Ind. Microbiol. Biotechnol. / Year: 2018
Title: Heterologous production of a new lasso peptide brevunsin in Sphingomonas subterranea
Authors: Kodani, S. / Hemmi, H. / Miyake, Y. / Kaweewan, I. / Nakagawa, H.
History
DepositionFeb 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: brevunsin


Theoretical massNumber of molelcules
Total (without water)2,2531
Polymers2,2531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1930 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 brevunsin


Mass: 2253.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Novosphingobium subterraneum (bacteria) / References: UniProt: F4QXD9, UniProt: A0A381AKI5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic22D 1H-13C HMBC
141isotropic22D 1H-1H TOCSY
151isotropic12D 1H-1H TOCSY
181isotropic22D DQF-COSY
171isotropic22D 1H-1H NOESY
161isotropic12D 1H-1H NOESY
191isotropic21D 1H
1101isotropic21D 13C
1111isotropic2DEPT135

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Sample preparation

DetailsType: solution / Contents: 6 mg/mL brevunsin, DMSO / Label: 1 / Solvent system: DMSO
SampleConc.: 6 mg/mL / Component: brevunsin / Isotopic labeling: natural abundance
Sample conditionsIonic strength: ND Not defined / Label: 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
TopSpin3.5Bruker Biospinprocessing
TopSpinBruker Biospincollection
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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