+Open data
-Basic information
Entry | Database: PDB / ID: 5y0j | ||||||
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Title | Solution structure of arenicin-3 derivative N2 | ||||||
Components | N2 | ||||||
Keywords | ANTIBIOTIC / arenicin-3 derivative beta-hairpin antimicrobial action | ||||||
Biological species | Arenicola marina (lugworm) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Liu, X.H. / Wang, J.H. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y0j.cif.gz | 120.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y0j.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 5y0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y0j_validation.pdf.gz | 504.3 KB | Display | wwPDB validaton report |
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Full document | 5y0j_full_validation.pdf.gz | 697.3 KB | Display | |
Data in XML | 5y0j_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 5y0j_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/5y0j ftp://data.pdbj.org/pub/pdb/validation_reports/y0/5y0j | HTTPS FTP |
-Related structure data
Related structure data | 5y0hC 5y0iC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2575.053 Da / Num. of mol.: 1 / Mutation: G1A,Y5N,G12A,Y17H / Source method: obtained synthetically / Source: (synth.) Arenicola marina (lugworm) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 2.0 mM NA- N2, 90% H2O/10% D2O / Label: NA- / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 2.0 mM / Component: N2 / Isotopic labeling: NA- |
Sample conditions | Ionic strength: 0 mM / Label: condition_1 / pH: 4 Not defined / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Agilent dd2 / Manufacturer: Agilent / Model: dd2 / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |