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Yorodumi- PDB-6qyv: Solution NMR of synthetic analogues of nisin and mutacin ring A a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qyv | ||||||
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Title | Solution NMR of synthetic analogues of nisin and mutacin ring A and ring B - Mutacin I Ring A (Ser2, Ala5, Ala8) analogue | ||||||
Components | PHE-SER-DAL-LEU-ALA-LEU-CYS-ALA | ||||||
Keywords | ANTIBIOTIC / PEPTIDE ANTIBIOTIC / LANTIBIOTIC / ANTIMICROBIAL / BACTERIOCIN / THIOESTER | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Dickman, R. / Mitchell, S.A. / Figueiredo, A. / Hansen, D.F. / Tabor, A.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Org.Chem. / Year: 2019 Title: Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B. Authors: Dickman, R. / Mitchell, S.A. / Figueiredo, A.M. / Hansen, D.F. / Tabor, A.B. #1: Journal: To Be Published Title: A chemical biology approach to understanding molecular recognition of lipid II by nisin: Solid-phase synthesis and NMR ensemble analysis of nisin(1-12) and a synthetic ana-logue. Authors: Dickman, R. / Danelius, E. / Mitchell, S.A. / Hansen, D.F. / Erdelyi, M. / Tabor, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qyv.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qyv.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qyv_validation.pdf.gz | 366 KB | Display | wwPDB validaton report |
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Full document | 6qyv_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 6qyv_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 6qyv_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/6qyv ftp://data.pdbj.org/pub/pdb/validation_reports/qy/6qyv | HTTPS FTP |
-Related structure data
Related structure data | 6qm1C 6qtfC 6qyrC 6qysC 6qytC 6qyuC 6qywC 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: 794.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria) |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: lyophilized powder Contents: 0.7 mg/mL Mutacin I Ring A (Ser2, Ala5, Ala8) analogue, DMSO Label: sample_1 / Solvent system: DMSO |
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Sample | Conc.: 0.7 mg/mL / Component: Mutacin I Ring A (Ser2, Ala5, Ala8) analogue / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: TFA salt Not defined / Label: DMSO_rt / pH: 5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | ||||||||||||||||||||
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: 15 |