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- PDB-6pi3: NMR Solution structure of native tachyplesin III peptide -

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Basic information

Entry
Database: PDB / ID: 6pi3
TitleNMR Solution structure of native tachyplesin III peptide
ComponentsTachyplesin-3
KeywordsANTIMICROBIAL PROTEIN / defense peptide
Function / homologydefense response to bacterium / extracellular region / Tachyplesin-3
Function and homology information
Biological speciesTachypleus gigas (Southeast Asian horseshoe crab)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Troeira Henriques, S. / Vernen, F.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Characterization of Tachyplesin Peptides and Their Cyclized Analogues to Improve Antimicrobial and Anticancer Properties.
Authors: Vernen, F. / Harvey, P.J. / Dias, S.A. / Veiga, A.S. / Huang, Y.H. / Craik, D.J. / Lawrence, N. / Troeira Henriques, S.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tachyplesin-3


Theoretical massNumber of molelcules
Total (without water)2,2451
Polymers2,2451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint0 kcal/mol
Surface area2070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Tachyplesin-3 / Tachyplesin III


Mass: 2244.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Tachypleus gigas (Southeast Asian horseshoe crab)
References: UniProt: P18252

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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 TOCSY
121isotropic12D 1H-1H NOESY
132isotropic12D E.COSY
141isotropic12D 1H-15N HSQC
152isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
lyophilized powder11.0 mg/mL tachyplesin III, 90% H2O/10% D2OtachyplesinIII_sample90% H2O/10% D2O
lyophilized powder21.0 mg/mL tachyplesin III, 100% D2Od2o_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mg/mLtachyplesin IIInatural abundance1
1.0 mg/mLtachyplesin IIInatural abundance2
Sample conditionsIonic strength: na Not defined / Label: conditions_1 / pH: 4 / 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
NameVersionDeveloperClassification
TopSpin3.6.1Bruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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