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Yorodumi- PDB-6gnz: Plantaricin S-a in 100 mM DPC micelles. This is the alpha part of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gnz | ||||||
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Title | Plantaricin S-a in 100 mM DPC micelles. This is the alpha part of the bacteriocin plantaricin S. | ||||||
Components | Plantaricin S alpha protein | ||||||
Keywords | ANTIMICROBIAL PROTEIN / ANTIMICROBIAL PROTEIN Bacteriocin menbrane interacting peptide | ||||||
Function / homology | Bacteriocin-type signal sequence / cytolysis / defense response to bacterium / Plantaricin S alpha protein Function and homology information | ||||||
Biological species | Lactobacillus plantarum (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Ekblad, B. / Kristiansen, P.E. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: NMR structures and mutational analysis of the two peptides constituting the bacteriocin plantaricin S. Authors: Ekblad, B. / Kristiansen, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gnz.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gnz.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/6gnz ftp://data.pdbj.org/pub/pdb/validation_reports/gn/6gnz | HTTPS FTP |
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-Related structure data
Related structure data | 6go0C 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: 2926.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactobacillus plantarum (bacteria) / References: UniProt: O32831 |
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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: bicelle Contents: 1 mM Plantaricin Sb, 0.2 mM DSS, 100 mM [U-100% 2H] DPC, 95% Label: Sample_1 / Solvent system: 95% | ||||||||||||||||
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Sample |
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Sample conditions | Details: Peptide purchased at 98% purity from genscript used as is. no buffers added to the DPC micelles Ionic strength: 0 Not defined / Label: condition 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz / Details: with cryoprobe |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: NOE and dihedral angle restraints used in refinement in dmso using the script ReCOORD | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |