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- PDB-5vl6: Peptide 38138 modified from fragment 21-37 of Plasmodium falcipar... -

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Basic information

Entry
Database: PDB / ID: 5vl6
TitlePeptide 38138 modified from fragment 21-37 of Plasmodium falciparum Cell-Traversal Protein for Ookinetes and Sporozoite (Pf-CelTOS)
ComponentsPeptide 38138
KeywordsCELL INVASION / Modified peptide / Chemically synthesized / Pf-CelTOS / Alpha helix residues 8-14
Function / homologyCell-traversal protein for ookinetes and sporozoites / Cell-traversal protein for ookinetes and sporozoites / Cell traversal protein for ookinetes and sporozoites
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBermudez, A. / Patarroyo, M.E.
CitationJournal: To Be Published
Title: Peptide 38138 modified from fragment 21-37 of Plasmodium falciparum Cell-Traversal Protein for Ookinetes and Sporozoite (Pf-CelTOS)
Authors: Bermudez, A. / Patarroyo, M.E.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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: Peptide 38138


Theoretical massNumber of molelcules
Total (without water)1,8741
Polymers1,8741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide 38138


Mass: 1873.959 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide 38138 modified from fragment 21-37 of Plasmodium falciparum Cell-Traversal Protein for Ookinetes and Sporozoite (Pf-CelTOS)
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8I5P1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D DQF-COSY; 2D 1H-1H TOCSY; 2D 1H-1H NOESY
221anisotropic12D 1H-1H TOCSY
331anisotropic12D 1H-1H TOCSY
441anisotropic12D 1H-1H TOCSY
NMR detailsText: NULL

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Sample preparation

DetailsType: solution / Contents: 16.6 mg/mL 38138, trifluoroethanol/water
Details: Peptide 38138 modified from fragment 21-37 of Plasmodium falciparum Cell-Traversal Protein for Ookinetes and Sporozoite (Pf-CelTOS)
Label: 38138 / Solvent system: trifluoroethanol/water
SampleConc.: 16.6 mg/mL / Component: 38138 / Isotopic labeling: natural abundance
Sample conditions

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

Conditions-IDDetailsLabelTemperature (K)
1TEMPERATURE AMBIENT38138 (295)295 K
2TEMPERATURE 285 K38138 (285)285 K
3TEMPERATURE 305 K38138 (305)305 K
4TEMPERATURE 315 K38138 (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
NameDeveloperClassification
Insight IIACCELRYS SOFTWARE INC.refinement
Insight IIstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: 193 NOES
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 9

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