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- PDB-2lx6: Structure of Lasso Peptide Caulosegnin I -

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Basic information

Entry
Database: PDB / ID: 2lx6
TitleStructure of Lasso Peptide Caulosegnin I
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / CAULOSEGNIN I / LASSO PEPTIDE / LARIAT PROTOKNOT
Function / homologyUncharacterized protein
Function and homology information
Biological speciesCaulobacter segnis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHegemann, J.D. / Zimmermann, M. / Xie, X. / Marahiel, M.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Caulosegnins I-III: A Highly Diverse Group of Lasso Peptides Derived from a Single Biosynthetic Gene Cluster.
Authors: Hegemann, J.D. / Zimmermann, M. / Xie, X. / Marahiel, M.A.
History
DepositionAug 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jun 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_spectrometer / 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_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)1,9401
Polymers1,9401
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Putative uncharacterized protein / CAULOSEGNIN I


Mass: 1940.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter segnis (bacteria)
Strain: ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059
Gene: CSEGA1, Cseg_2568 / Plasmid: PET41A / Production host: CAULOBACTER SEGNIS (bacteria) / References: UniProt: D5VKJ9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D DQF-COSY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 10 mM CAULOSEGNIN I, methanol / Solvent system: methanol
SampleConc.: 10 mM / Component: CAULOSEGNIN I-1
Sample conditionsPressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 148 / NOE intraresidue total count: 74 / NOE long range total count: 26 / NOE medium range total count: 2 / NOE sequential total count: 36
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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