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- PDB-5tj1: Benenodin-1-dC5, state 1 -

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Basic information

Entry
Database: PDB / ID: 5tj1
TitleBenenodin-1-dC5, state 1
ComponentsBenenodin-1
KeywordsUNKNOWN FUNCTION / Lasso peptide RiPPs
Function / homologyBenenodin family lasso peptide
Function and homology information
Biological speciesAsticcacaulis benevestitus DSM 16100 = ATCC BAA-896 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsZong, C. / Link, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107036 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch.
Authors: Zong, C. / Wu, M.J. / Qin, J.Z. / Link, A.J.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benenodin-1


Theoretical massNumber of molelcules
Total (without water)2,0331
Polymers2,0331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Benenodin-1


Mass: 2033.308 Da / Num. of mol.: 1 / Fragment: UNP residues 22-40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896 (bacteria)
Gene: ABENE_08090 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: V4RMX4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: 2D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 2.50 mg/mL NA Benenodin-1-dC5, state 1, 90% H2O/10% D2O
Label: Benenodin-1-dC5, state 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.50 mg/mL / Component: Benenodin-1-dC5, state 1 / Isotopic labeling: NA
Sample conditionsIonic strength: 1 mM / Label: Benenodin-1-dC5, state 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
Mnova8Mestrelab Researchchemical shift assignment
GROMACSHerman Berendsen's grouprefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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