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- PDB-6ct4: TFE-induced NMR structure of an antimicrobial peptide (EcDBS1R5) ... -

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Basic information

Entry
Database: PDB / ID: 6ct4
TitleTFE-induced NMR structure of an antimicrobial peptide (EcDBS1R5) derived from a mercury transporter protein (MerP - Escherichia coli)
ComponentsEcDBS1R5
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial peptide / Antibiotics / Bacterial resistance / Drug design
Function / homologyMerP protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsCardoso, M.H. / Chan, L.Y. / Candido, E.S. / 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: ACS Infect Dis / Year: 2018
Title: A Computationally Designed Peptide Derived from Escherichia coli as a Potential Drug Template for Antibacterial and Antibiofilm Therapies.
Authors: Cardoso, M.H. / Candido, E.S. / Chan, L.Y. / Der Torossian Torres, M. / Oshiro, K.G.N. / Rezende, S.B. / Porto, W.F. / Lu, T.K. / de la Fuente-Nunez, C. / Craik, D.J. / Franco, O.L.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EcDBS1R5


Theoretical massNumber of molelcules
Total (without water)2,1531
Polymers2,1531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2320 Å2
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 EcDBS1R5 / MerP protein


Mass: 2152.794 Da / Num. of mol.: 1 / Mutation: synthetic construct / Source method: obtained synthetically / Details: Mercury ion transport protein-derived peptide / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: O06514

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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 EcDBS1R5, 30 % na TFE, 60 % na H2O, 10 % na D2O, 10 % na DSS, trifluoroethanol/water
Details: Synthetic peptide in water/TFE mixture / Label: EcDBS1R5 / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEcDBS1R5na1
30 %TFEna1
60 %H2Ona1
10 %D2Ona1
10 %DSSna1
Sample conditionsIonic strength: 0 Not defined / Label: EcDBS1R5_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 Wuthrichdata analysis
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: 200 / Conformers submitted total number: 10

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