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- PDB-7mn3: Homotarsinin monomer - Htr-M -

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Basic information

Entry
Database: PDB / ID: 7mn3
TitleHomotarsinin monomer - Htr-M
ComponentsHomotarsinin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homologydefense response to bacterium / extracellular region / Homotarsinin
Function and homology information
Biological speciesPhyllomedusa tarsius (brownbelly leaf frog)
MethodSOLUTION NMR / simulated annealing
AuthorsVerly, R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Minas Gerais State Agency for Research and Development (FAPEMIG) Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Sci Rep / Year: 2017
Title: Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin.
Authors: Verly, R.M. / Resende, J.M. / Junior, E.F. / de Magalhaes, M.T. / Guimaraes, C.F. / Munhoz, V.H. / Bemquerer, M.P. / Almeida, F.C. / Santoro, M.M. / Pilo-Veloso, D. / Bechinger, B.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homotarsinin


Theoretical massNumber of molelcules
Total (without water)2,7591
Polymers2,7591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Homotarsinin


Mass: 2759.427 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Phyllomedusa tarsius (brownbelly leaf frog)
References: UniProt: P84337
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC NH2 only
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 4.0 mM Htr-M, trifluoroethanol/water / Details: TFE-d2/H2O (30/70, v/v) / Label: natural abundace / Solvent system: trifluoroethanol/water
SampleConc.: 4.0 mM / Component: Htr-M / Isotopic labeling: natural abundance
Sample conditionsDetails: TFE-d2/H2O (30/70, v/v) / Ionic strength: 0 Not defined / Label: TFE-d2/H2O / pH: 7.0 pH* / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
QUEENNabuurs, Spronk, Krieger, Maassen, Vriend and Vuisterdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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