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- PDB-2n9r: Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal ... -

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Basic information

Entry
Database: PDB / ID: 2n9r
TitleNovel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics
ComponentsAntimicrobial peptide PaDBS1R1
KeywordsANTIMICROBIAL PROTEIN
Function / homologyRibosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / Large ribosomal subunit protein eL39
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsIrazazabal, L.S.F. / Porto, W.F. / Alves, E.S.F. / Matos, C.O. / Hancock, R.E.W. / Haney, E. / Ribeiro, S.M. / Liao, L.M. / Ladram, A.S.F. / Franco, O.L.
CitationJournal: To be Published
Title: Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics
Authors: Alves, E.S.F. / Matos, C.O. / Liao, L.M.
History
DepositionDec 3, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antimicrobial peptide PaDBS1R1


Theoretical massNumber of molelcules
Total (without water)2,1111
Polymers2,1111
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Antimicrobial peptide PaDBS1R1


Mass: 2110.717 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics
Source: (synth.) synthetic construct (others) / References: UniProt: Q8ZTX6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Active against gram-positive and negative bacteria
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC
1412D 1H-15N sfHMQC

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Sample preparation

DetailsContents: 5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
5 %TSP-11
10 %D2O-21
90 %H2O-31
100 mMSDS-41
30 mMsodium phosphate-51
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR_NIH2.28Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIH2.28Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxdata analysis
QUEENNabuurs, Spronk, Krieger, Maassen, Vriend and Vuisterdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
MolmolKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: In the final step was performed refinement in water
NMR constraintsNOE constraints total: 244 / NOE intraresidue total count: 175 / NOE long range total count: 0 / NOE medium range total count: 18 / NOE sequential total count: 84
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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