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- PDB-1s7p: Solution structure of thermolysin digested microcin J25 -

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Basic information

Entry
Database: PDB / ID: 1s7p
TitleSolution structure of thermolysin digested microcin J25
Components(microcin J25) x 2
KeywordsANTIBIOTIC / thermolysin digested microcin J25 / t-Mccj25 / thermolysin digest / two-chain peptide / steric link / ANTIMICROBIAL PROTEIN
Function / homologykilling of cells of another organism / defense response to bacterium / extracellular region / Microcin J25
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Structures were calculated using torsion angle dynamics in CNS, refined in explicit solvent.
AuthorsRosengren, K.J. / Blond, A. / Afonso, C. / Tabet, J.C. / Rebuffat, S. / Craik, D.J.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of thermolysin cleaved microcin J25: extreme stability of a two-chain antimicrobial peptide devoid of covalent links
Authors: Rosengren, K.J. / Blond, A. / Afonso, C. / Tabet, J.C. / Rebuffat, S. / Craik, D.J.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: microcin J25
A: microcin J25


Theoretical massNumber of molelcules
Total (without water)2,1442
Polymers2,1442
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)20 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide microcin J25


Mass: 1110.261 Da / Num. of mol.: 1 / Fragment: Residues 48-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: DIGESTED WITH THERMOLYSIN; / Gene: mcj25A / Plasmid: pTUC202 / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: Q9X2V7
#2: Protein/peptide microcin J25


Mass: 1034.102 Da / Num. of mol.: 1 / Fragment: Residues 38-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: digested with thermolysin / Gene: mcj25A / Plasmid: pTUC202 / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: Q9X2V7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 6mM t-MccJ25 / Solvent system: 100% CD3OH
Sample conditionsIonic strength: 0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR2.6Brukercollection
XEASY1.3.7Eccles et al.data analysis
CNS1Brunger et al.structure solution
CNS1Brunger et al.refinement
RefinementMethod: Structures were calculated using torsion angle dynamics in CNS, refined in explicit solvent.
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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