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- PDB-5y0i: Solution structure of arenicin-3 derivative N1 -

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Basic information

Entry
Database: PDB / ID: 5y0i
TitleSolution structure of arenicin-3 derivative N1
ComponentsNZ17074(N1)
KeywordsANTIBIOTIC / arenicin-3 derivative beta-hairpin antimicrobial action
Biological speciesArenicola marina (lugworm)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, X.H. / Wang, J.H.
CitationJournal: Sci Rep / Year: 2017
Title: Antibacterial and detoxifying activity of NZ17074 analogues with multi-layers of selective antimicrobial actions against Escherichia coli and Salmonella enteritidis
Authors: Yang, N. / Liu, X. / Teng, D. / Li, Z. / Wang, X. / Mao, R. / Wang, X.M. / Hao, Y. / Wang, J.
History
DepositionJul 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NZ17074(N1)


Theoretical massNumber of molelcules
Total (without water)2,5471
Polymers2,5471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide NZ17074(N1)


Mass: 2547.001 Da / Num. of mol.: 1 / Mutation: Y5N, Y17H / Source method: obtained synthetically / Source: (synth.) Arenicola marina (lugworm)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 2.0 mM NA- NZ17074(N1), 90% H2O/10% D2O / Label: NA- / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.0 mM / Component: NZ17074(N1) / Isotopic labeling: NA-
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 4 / Pressure: 1.0 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMRCCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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