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- PDB-2lti: Structure of lasso peptide Astexin1 -

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Basic information

Entry
Database: PDB / ID: 2lti
TitleStructure of lasso peptide Astexin1
ComponentsASTEXIN1
KeywordsANTIMICROBIAL PROTEIN / ASTEXIN1 / SIDECHAIN-TO-BACKBONE LINK / LASSO PEPTIDE
Function / homologydefense response to bacterium / Astexin-1
Function and homology information
Biological speciesAsticcacaulis excentricus (bacteria)
MethodSOLUTION NMR / STRUCTURES WERE CALCULATED BY TORSION ANGLE DYNAMICS, SIMULATED ANNEALING.
AuthorsMaksimov, M.O. / Link, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Precursor-centric genome-mining approach for lasso peptide discovery.
Authors: Maksimov, M.O. / Pelczer, I. / Link, A.J.
History
DepositionMay 25, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASTEXIN1


Theoretical massNumber of molelcules
Total (without water)2,5841
Polymers2,5841
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 LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ASTEXIN1


Mass: 2583.697 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: Astex_2228 / Plasmid: PASK-75 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E8RMD3

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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

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Sample preparation

DetailsContents: 4.4 mg/mL ASTEXIN1, DMSO / Solvent system: DMSO
SampleConc.: 4.4 mg/mL / Component: ASTEXIN1-1
Sample conditionsPressure: AMBIENT / Temperature: 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
CYANA2.1GUNTERT, MUMENTHALER AND WUTHRICHrefinement
TopSpin2.1Bruker Biospincollection
MESTRENOVA7.0.3Mestrelab Researchdata analysis
Tinker6PONDERrefinement
RefinementMethod: STRUCTURES WERE CALCULATED BY TORSION ANGLE DYNAMICS, SIMULATED ANNEALING.
Software ordinal: 1
Details: AN ENSEMBLE OF 200 STRUCTURES WAS GENERATED BY SIMULATED ANNEALING UNDER A SET OF 144 NOE DERIVED UPPER DISTANCE RESTRAINTS AND 5 3JHHA COUPLING DERIVED PHI ANGLE RESTRAINTS. 20 LOWEST ...Details: AN ENSEMBLE OF 200 STRUCTURES WAS GENERATED BY SIMULATED ANNEALING UNDER A SET OF 144 NOE DERIVED UPPER DISTANCE RESTRAINTS AND 5 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 LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 200 / Conformers submitted total number: 20

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