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- PDB-2bbx: NMR solution structure of the TSR domain of malaria TRAP protein -

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Basic information

Entry
Database: PDB / ID: 2bbx
TitleNMR solution structure of the TSR domain of malaria TRAP protein
ComponentsThrombospondin-related anonymous protein
KeywordsCELL ADHESION / elongated three-stranded structure
Function / homology
Function and homology information


heparin binding / membrane => GO:0016020 / cell adhesion / plasma membrane
Similarity search - Function
Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Thrombospondin-related anonymous protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / simulated annealing
AuthorsTossavainen, H. / Permi, P. / Kilpelainen, I.
CitationJournal: Protein Sci. / Year: 2006
Title: The layered fold of the TSR domain of P. falciparum TRAP contains a heparin binding site.
Authors: Tossavainen, H. / Pihlajamaa, T. / Huttunen, T.K. / Raulo, E. / Rauvala, H. / Permi, P. / Kilpelainen, I.
History
DepositionOct 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombospondin-related anonymous protein


Theoretical massNumber of molelcules
Total (without water)5,4501
Polymers5,4501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Thrombospondin-related anonymous protein / TRAP


Mass: 5450.023 Da / Num. of mol.: 1 / Fragment: TSP domain type 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: TRAP / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P16893

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques.

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Sample preparation

DetailsContents: 0.5 mM TRAP-TSR U-15N,13C; 20 mM bis-Tris buffer / Solvent system: 94% H20, 6% D2O
Sample conditionsIonic strength: na / pH: 6.6 / Pressure: ambient / Temperature: 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVarian Inc.collection
Sparky3.106Goddard TD & Kneller DGdata analysis
CYANA1Guntert Pstructure solution
Amber8Case DA et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 754 NOE-derived distance constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 20

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