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- PDB-2m37: Structure of lasso peptide astexin-1 -

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Basic information

Entry
Database: PDB / ID: 2m37
TitleStructure of lasso peptide astexin-1
ComponentsASTEXIN-1
KeywordsUNKNOWN FUNCTION / ASTEXIN-1 / LASSO PEPTIDE / LARIAT PROTOKNOT
Function / homologydefense response to bacterium / Astexin-1
Function and homology information
Biological speciesAsticcacaulis excentricus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZimmermann, M. / Hegemann, J.D. / Xie, X. / Marahiel, M.A.
CitationJournal: Chem.Biol. / Year: 2013
Title: The astexin-1 lasso peptides: biosynthesis, stability, and structural studies.
Authors: Zimmermann, M. / Hegemann, J.D. / Xie, X. / Marahiel, M.A.
History
DepositionJan 14, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASTEXIN-1


Theoretical massNumber of molelcules
Total (without water)2,1131
Polymers2,1131
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ASTEXIN-1


Mass: 2113.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asticcacaulis excentricus (bacteria) / Strain: ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48 / Gene: ATXA / Strain (production host): CB48 / References: UniProt: E8RMD3
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-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 5.7 mM ASTEXIN-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 5.7 mM / Component: ASTEXIN-1(19)-1
Sample conditionsPressure: ambient atm / Temperature: 283 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
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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