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- PDB-6csz: TFE-induced NMR structure of a novel bioactive peptide (PaDBS1R3)... -

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Basic information

Entry
Database: PDB / ID: 6csz
TitleTFE-induced NMR structure of a novel bioactive peptide (PaDBS1R3) derived from a Pyrobaculum aerophilum ribosomal protein (L39e)
ComponentsPaDBS1R3
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptide / Antibiotics / Bacterial Resistance / Cationic Peptide
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 speciesPyrobaculum aerophilum (archaea)
MethodSOLUTION NMR / molecular dynamics
AuthorsCardoso, M.H. / Chan, L.Y. / Candido, E.S. / Torres, M.T. / Oshiro, K.G.N. / Silva, I.C. / Goncalves, S. / Buccini, D.F. / Lu, T. / Santos, N.C. ...Cardoso, M.H. / Chan, L.Y. / Candido, E.S. / Torres, M.T. / Oshiro, K.G.N. / Silva, I.C. / Goncalves, S. / Buccini, D.F. / Lu, T. / Santos, N.C. / de la Fuente-Nunez, C. / Craik, D.J. / Franco, O.L.
Funding support Australia, Brazil, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL150100146 Australia
Brazilian National Council for Scientific and Technological Development (CNPq)141518/2015-4 Brazil
CitationJournal: Chem Sci / Year: 2022
Title: An N-capping asparagine-lysine-proline (NKP) motif contributes to a hybrid flexible/stable multifunctional peptide scaffold
Authors: Cardoso, M.H. / Chan, L.Y. / Candido, E.S. / Buccini, D.F. / Rezende, S.B. / Torres, M.D.T. / Oshiro, K.G.N. / Silva, I.C. / Goncalves, S. / Lu, T.K. / Santos, N.C. / de la Fuente-Nunez, C. ...Authors: Cardoso, M.H. / Chan, L.Y. / Candido, E.S. / Buccini, D.F. / Rezende, S.B. / Torres, M.D.T. / Oshiro, K.G.N. / Silva, I.C. / Goncalves, S. / Lu, T.K. / Santos, N.C. / de la Fuente-Nunez, C. / Craik, D.J. / Franco, O.L.
History
DepositionMar 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 7, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PaDBS1R3


Theoretical massNumber of molelcules
Total (without water)2,1441
Polymers2,1441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2180 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PaDBS1R3 / 50S ribosomal protein L39e


Mass: 2143.807 Da / Num. of mol.: 1 / Fragment: UNP residues 1-18 / Mutation: synthetic construct / Source method: obtained synthetically / Source: (synth.) Pyrobaculum aerophilum (archaea) / References: UniProt: Q8ZTX6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H TOCSY
121anisotropic12D 1H-1H NOESY
131anisotropic12D 1H-15N HSQC
141anisotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM na PaDBS1R3, 30 % na TFE, 60 % na H2O, 10 % na D2O, 10 % na DSS, trifluoroethanol/water
Details: Synthetic peptide in water/TFE mixture / Label: PaDBS1R3 / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPaDBS1R3na1
30 %TFEna1
60 %H2Ona1
10 %D2Ona1
10 %DSSna1
Sample conditionsDetails: Synthetic peptide in water/TFE mixture / Ionic strength: 0 Not defined / Label: PaDBS1R3_TFE / pH: 4.3 / Pressure: 1 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 software
NameDeveloperClassification
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichchemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6 / Details: with simulated annealing; refinement in water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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