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- PDB-2gjy: NMR Solution Structure of Tensin1 PTB Domain -

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Basic information

Entry
Database: PDB / ID: 2gjy
TitleNMR Solution Structure of Tensin1 PTB Domain
ComponentsTensin
KeywordsCELL ADHESION / focal adhesion beta sandwich
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / fibroblast migration / phosphoprotein phosphatase activity / actin binding / cytoskeleton / focal adhesion / cell surface / cytoplasm
Similarity search - Function
Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein ...Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / C2 domain superfamily / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics energy minimization
AuthorsLeone, M. / Pellecchia, M.
CitationJournal: Biopolymers / Year: 2007
Title: The PTB domain of tensin: NMR solution structure and phosphoinositides binding studies.
Authors: Leone, M. / Yu, E.C. / Liddington, R.C. / Pasquale, E.B. / Pellecchia, M.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 9, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tensin


Theoretical massNumber of molelcules
Total (without water)15,6701
Polymers15,6701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Tensin /


Mass: 15669.822 Da / Num. of mol.: 1 / Fragment: PTB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TNS / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q04205

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1333D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM PTB domain U-15N; 50mM phosphate buffer; 150mM NaCl; 90%H2O; 10%D2O50mM phosphate buffer; 150mM NaCl; 90% H2O; 10%D2O
21mM PTB domain U-15N; 50mM phosphate buffer; 150mM NaCl; 100%D2O50mM phosphate buffer; 150mM NaCl; 100%D2O
31mM PTB domain U-15N, U-13C; 50mM phosphate buffer; 150mM NaCl; 90%H2O, 10%D2O50mM phosphate buffer; 150mM NaCl; 90%H2O; 10%D2O
Sample conditionsIonic strength: 50mM phosphate and 150mM NaCl / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Gunthertstructure solution
GROMOS96Van Gunsterenrefinement
XwinNMR3.5Brukerprocessing
XEASY1.3.13Bartelsdata analysis
RefinementMethod: torsion angle dynamics energy minimization / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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