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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
TitleStructure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot
Componentsmicrocin J25
KeywordsANTIBIOTIC / LARIAT / PROTOKNOT / BACKBONE-SIDECHAIN AMIDE LINKAGE / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologykilling of cells of another organism / defense response to bacterium / extracellular region / Microcin J25 / Microcin J25
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsBayro, 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)
CitationJournal: J.Am.Chem.Soc. / Year: 2003
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
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 6, 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 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: microcin J25


Theoretical massNumber of molelcules
Total (without water)2,1261
Polymers2,1261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide microcin J25


Type: Polypeptide / Class: Inhibitor / Mass: 2126.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MCJA / Plasmid: pTUC202 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9X2V7, Microcin J25
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
141HN(CA)CB
151CBCA(CO)NH
161
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2mM Microcin J25 U-13C,15N; 99.5% CD3OH, 0.5% H2O / Solvent system: 99.5% CD3OH, 0.5% H2O
Sample conditionsIonic strength: NA / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
AutoProc0.8Bayro, M.J.; Monleon, D.; Baran, M.C.; Sahota, G.; Paranji, R.; Moseley, H.N.B.; Aramini, J.M.; Swapna, G.V.T.; Montelione, G.T.processing
NMRPipe1.4Delaglio, F.; Grzesiek, S.; Vuister, G.; Zhu, G.; Pfeifer, J.; Bax, A.processing
AutoStructure1.1.2Huang, Y.J., Tejero, R., Montelione, G.T.structure solution
DYANA1.5Guntert, P.; Mumenthaler, C.; Wuthrich, K.structure solution
PdbStat3.25Tejero, R.; Montelione, G.T.refinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

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