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- PDB-2m8f: Structure of lasso peptide astexin3 -

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Basic information

Entry
Database: PDB / ID: 2m8f
TitleStructure of lasso peptide astexin3
Componentsastexin3
KeywordsUNKNOWN FUNCTION / sidechain-to-backbone link
Function / homologydefense response to bacterium / extracellular region / cytoplasm / Astexin-3
Function and homology information
Biological speciesAsticcacaulis excentricus (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsMaksimov, M.O. / Link, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Discovery and characterization of an isopeptidase that linearizes lasso peptides.
Authors: Maksimov, M.O. / Link, A.J.
History
DepositionMay 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 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_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 27, 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: astexin3


Theoretical massNumber of molelcules
Total (without water)2,5431
Polymers2,5431
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide astexin3


Mass: 2542.755 Da / Num. of mol.: 1 / Fragment: UNP residues 26-49
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: Astex_2447 / Plasmid: pASK-75 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: E8RUP8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1312D COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 16.25 mg/mL astexin3, DMSO / Solvent system: DMSO
SampleConc.: 16.25 mg/mL / Component: astexin3-1
Sample conditionsTemperature: 295 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA6Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin2.1Ponderprocessing
MESTRENOVA7.0.3MestreLab Research, S.S.L., Santiago de Compostella, Spainprocessing
Tinker6Ponderrefinement
CYANA6Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: An ensemble of 200 structures was generated by simulated annealing under a set of 218 NOE-derived upper distance restraints and 11 3JHHA coupling-derived phi angle restraints. 20 lowest ...Details: An ensemble of 200 structures was generated by simulated annealing under a set of 218 NOE-derived upper distance restraints and 11 3JHHA coupling-derived phi angle restraints. 20 lowest energy structures were refined further by energy minimization using TINKER 6.0.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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