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- PDB-5uy2: peptide 38146 derived from fragment 41-60 of Plasmodium falciparu... -

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Basic information

Entry
Database: PDB / ID: 5uy2
Titlepeptide 38146 derived from fragment 41-60 of Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
Components20-mer Peptide 38146
KeywordsCELL INVASION / Derived peptide / Chemically synthesized / Pf-TRSP protein / Alfa-helix residues 11-18.
Function / homologyCCN, TSP1 domain / CCN3 Nov like TSP1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / signal transduction / plasma membrane / Thrombospondin-related sporozoite protein
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodSOLUTION NMR / DGSA-DISTANCE GEOMETRY SIMULATED A
AuthorsBermudez, A. / Patarroyo, M.E.
CitationJournal: To Be Published
Title: peptide 38146 derived from fragment 41-60 of Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
Authors: Bermudez, A. / Patarroyo, M.E.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: 20-mer Peptide 38146


Theoretical massNumber of molelcules
Total (without water)2,4601
Polymers2,4601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 20-mer Peptide 38146


Mass: 2459.632 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: fragment 41-60 of Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I2A0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
131anisotropic12D DFQ-COSY, 2D 1H-1H TOCSY, 2D 1H-1H NOESY
241anisotropic12D 1H-1H TOCSY
361anisotropic12D 1H-1H TOCSY
451anisotropic12D 1H-1H TOCSY
NMR detailsText: NULL

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Sample preparation

DetailsType: solution / Contents: 16.6 mg/mL 38145, trifluoroethanol/water
Details: Peptide 38145 derived from Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
Label: 38145 / Solvent system: trifluoroethanol/water
SampleConc.: 16.6 mg/mL / Component: 38145 / Isotopic labeling: natural abundance
Sample conditions

Ionic strength: NULL Not defined / pH: 3.7 / PH err: 0.1 / Pressure: AMBIENT / Temperature err: 0.1

Conditions-IDDetailsLabelTemperature (K)
1Temperature ambient38145(295)295 K
2Temperature 285K38145(285)285 K
3Temperature 305K38145(305)305 K
4Temperature 315K38145(315)315 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameClassification
TopSpinrefinement
Insight IIstructure solution
RefinementMethod: DGSA-DISTANCE GEOMETRY SIMULATED A / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 24

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