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- PDB-1ma4: Solution Structure of Tachyplesin I Mutant TPY4 in water -

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Basic information

Entry
Database: PDB / ID: 1ma4
TitleSolution Structure of Tachyplesin I Mutant TPY4 in water
ComponentsTachyplesin 1
KeywordsANTIMICROBIAL PROTEIN / Tachyplesin I / Beta Hairpin / Tyrosine Mutant / TPY4
Function / homologydefense response to bacterium / extracellular region / Tachyplesin-1
Function and homology information
MethodSOLUTION NMR / Simulated Annealing with complete cross-validation
Model type detailsminimized average
AuthorsLaederach, A. / Andreotti, A.H. / Fulton, D.B.
CitationJournal: Biochemistry / Year: 2002
Title: Solution and micelle-bound structures of Tachyplesin I and its active linear derivatives
Authors: Laederach, A. / Andreotti, A.H. / Fulton, D.B.
History
DepositionJul 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tachyplesin 1


Theoretical massNumber of molelcules
Total (without water)2,5151
Polymers2,5151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 300structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Tachyplesin 1


Mass: 2514.931 Da / Num. of mol.: 1 / Mutation: C3Y C7Y C12Y C16Y / Source method: obtained synthetically
Details: The peptide was chemically synthesized using Fmoc solid state synthesis. The sequence of the peptide is naturally found in Tachypleus Tridentatus (Japanese Horeshoe Crab).
References: UniProt: P14213

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: For reasons of overlap, data was collected at both 298K and 277K. NOEs from spectra at both temperatures were used.

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Sample preparation

DetailsContents: TPY4 17 residue peptide
Solvent system: 90%/10% H2O/D2O and 99% D2O with 0.15% TFA, pH 3.0
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15% 3ambient 298 K
20.15% 3ambient 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, Adams, Clore, DeLano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure solution
XwinNMR6.1Brukercollection
XwinNMR6.1Brukerprocessing
CNS1Brunger, Adams, Clore, DeLano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenrefinement
RefinementMethod: Simulated Annealing with complete cross-validation / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 31

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