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- PDB-2n68: Solution study of Astexin1 -

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Basic information

Entry
Database: PDB / ID: 2n68
TitleSolution study of Astexin1
Componentsastexin1
KeywordsUNKNOWN FUNCTION
Function / homologydefense response to bacterium / Astexin-1
Function and homology information
Biological speciesAsticcacaulis excentricus CB 48 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsLink, A.J. / Maksimov, M.O.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Construction of Lasso Peptide Fusion Proteins.
Authors: Zong, C. / Maksimov, M.O. / Link, A.J.
History
DepositionAug 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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
Revision 1.4May 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: 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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide astexin1 / Lasso Peptide


Mass: 2583.697 Da / Num. of mol.: 1 / Fragment: unp residues 29-51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asticcacaulis excentricus CB 48 (bacteria)
Strain: CB 48 / Gene: Astex_2228 / 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 / Details: LASSO PEPTIDE, ANTIMICROBIAL PEPTIDE
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 7.27 mg/mL astexin1, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 7.27 mg/mL / Component: astexin1-1
Sample conditionsPressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Mestrenova9.0.0Mestrelab Researchdata analysis
GROMACS4.6.5Hess, Kutzner, van der Spoel and Lindahlrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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