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- PDB-6q1x: Lasso peptide pandonodin -

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Basic information

Entry
Database: PDB / ID: 6q1x
TitleLasso peptide pandonodin
ComponentsPandonodin
KeywordsUNKNOWN FUNCTION / Lasso peptide / RiPPs
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPandoraea norimbergensis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLink, A.J. / Cheung-Lee, W.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107036 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Pandonodin: A Proteobacterial Lasso Peptide with an Exceptionally Long C-Terminal Tail.
Authors: Cheung-Lee, W.L. / Cao, L. / Link, A.J.
History
DepositionAug 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
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: Pandonodin


Theoretical massNumber of molelcules
Total (without water)3,3311
Polymers3,3311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Pandonodin


Mass: 3330.956 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Isopeptide bond between N-terminus and Glu-8 side chain
Source: (gene. exp.) Pandoraea norimbergensis (bacteria) / Gene: AT302_15525 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0U2WJJ9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D gCOSY
121isotropic12D TOCSY
131isotropic12D NOESY
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 6 mg/mL pandonodin, Methanol-d3 / Label: 1 / Solvent system: Methanol-d3
SampleConc.: 6 mg/mL / Component: pandonodin / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 295 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
MestreLab (Mnova / MestReNova / MestReC)11Mestrelab Researchprocessing
MestreLab (Mnova / MestReNova / MestReC)11Mestrelab Researchchemical shift assignment
MestreLab (Mnova / MestReNova / MestReC)11Mestrelab Researchpeak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 18

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