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- PDB-2mmt: Lasso peptide-based integrin inhibitor: Microcin J25 variant with... -

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Entry
Database: PDB / ID: 2mmt
TitleLasso peptide-based integrin inhibitor: Microcin J25 variant with RGDF substitution of Gly12-Ile13-Gly14-Thr15
ComponentsMicrocin J25 RGDF mutant
KeywordsANTIBIOTIC / lasso peptide / epitope grafting / integrin inhibitor / drug design / molecular scaffolds / molecular dynamics
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 / simulated annealing
Model detailslowest energy, model1
AuthorsHegemann, J.D. / Zimmermann, M. / Knappe, T.A. / Xie, X. / Marahiel, M.A.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Rational improvement of the affinity and selectivity of integrin binding of grafted lasso peptides.
Authors: Hegemann, J.D. / De Simone, M. / Zimmermann, M. / Knappe, T.A. / Xie, X. / Di Leva, F.S. / Marinelli, L. / Novellino, E. / Zahler, S. / Kessler, H. / Marahiel, M.A.
History
DepositionMar 18, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microcin J25 RGDF mutant


Theoretical massNumber of molelcules
Total (without water)2,2741
Polymers2,2741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Microcin J25 RGDF mutant / MccJ25(RGDF)


Mass: 2274.490 Da / Num. of mol.: 1 / Fragment: UNP residues 38-58 / Mutation: G12R/I13G/G14D/T15F / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q9X2V7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 12.6 mM MCCJ25(RGDF), methanol / Solvent system: methanol
SampleConc.: 12.6 mM / Component: MCCJ25(RGDF)-1
Sample conditionsPressure: 1.0 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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