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- PDB-6wux: NMR soltution structure of homotarsinin homodimer - Htr -

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Basic information

Entry
Database: PDB / ID: 6wux
TitleNMR soltution structure of homotarsinin homodimer - Htr
ComponentsHomotarsinin
KeywordsANTIMICROBIAL PROTEIN / antmicrobial 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
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
B: Homotarsinin


Theoretical massNumber of molelcules
Total (without water)5,5192
Polymers5,5192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area3840 Å2
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.: 2 / Source method: obtained synthetically
Source: (synth.) Phyllomedusa tarsius (brownbelly leaf frog)
References: UniProt: P84337
Has ligand of interestY
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: 1 mM Homotarsinin - Htr, trifluoroethanol/water
Details: Htr at 1.0 mM in 20 mM, pH 7.0, phosphate buffer containing 5% TFE-d2
Label: natural abundance / Solvent system: trifluoroethanol/water
SampleConc.: 1 mM / Component: Homotarsinin - Htr / Isotopic labeling: natural abundance
Sample conditionsDetails: Htr at 1.0 mM in 20 mM, pH 7.0, phosphate buffer containing 5% TFE-d2
Ionic strength: 0 Not defined / Label: trifluoroethanol/water / 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: 800 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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