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- PDB-1pp5: Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lar... -
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Basic information
Entry | Database: PDB / ID: 1pp5 | ||||||
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Title | Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot | ||||||
![]() | microcin J25 | ||||||
![]() | ANTIBIOTIC / LARIAT / PROTOKNOT / BACKBONE-SIDECHAIN AMIDE LINKAGE / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | killing of cells of another organism / defense response to bacterium / extracellular region / Microcin J25 / Microcin J25![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Bayro, M.J. / Swapna, G.V.T. / Huang, J.Y. / Ma, L.-C. / Mukhopadhyay, J. / Ebright, R.H. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Structure of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot. Authors: Bayro, M.J. / Mukhopadhyay, J. / Swapna, G.V.T. / Huang, J.Y. / Ma, L.-C. / Sineva, E. / Dawson, P.E. / Montelione, G.T. / Ebright, R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.9 KB | Display | ![]() |
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PDB format | ![]() | 41.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 338.6 KB | Display | ![]() |
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Full document | ![]() | 401.1 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
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Sample preparation
Details | Contents: 2mM Microcin J25 U-13C,15N; 99.5% CD3OH, 0.5% H2O / Solvent system: 99.5% CD3OH, 0.5% H2O |
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Sample conditions | Ionic strength: NA / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The ensemble of structures is based on a total of 198 conformationally restraining constraints, 179 are NOE-derived distance constraints, 13 are dihedral angle constraints, 6 are distance ...Details: The ensemble of structures is based on a total of 198 conformationally restraining constraints, 179 are NOE-derived distance constraints, 13 are dihedral angle constraints, 6 are distance constraints from hydrogen bonds. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 60 / Conformers submitted total number: 10 |