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- PDB-6gbd: Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain -

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Basic information

Entry
Database: PDB / ID: 6gbd
TitleMurine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain
ComponentsPDZ3
KeywordsPROTEIN BINDING / PTPN13 / PDZ3
Function / homology
Function and homology information


RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / Synthesis of PIPs at the plasma membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity ...RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / Synthesis of PIPs at the plasma membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / lamellipodium / midbody / cytoskeleton / nucleus / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKock, G. / Stoll, R.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Molecular Basis of Class III Ligand Recognition by PDZ3 in Murine Protein Tyrosine Phosphatase PTPN13.
Authors: Kock, G. / Dicks, M. / Yip, K.T. / Kohl, B. / Putz, S. / Heumann, R. / Erdmann, K.S. / Stoll, R.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDZ3


Theoretical massNumber of molelcules
Total (without water)12,6901
Polymers12,6901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein PDZ3


Mass: 12690.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q64512

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
141isotropic13D 1H-15N NOESY
111isotropic13D 1H-13C NOESY
121isotropic13D (H)CCH-TOCSY
132isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] PDZ3, 90% H2O/10% D2O15N13_sample90% H2O/10% D2O
solution20.5 mM [U-99% 15N] PDZ3, 90% H2O/10% D2O15N_sampe90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMPDZ3[U-99% 13C; U-99% 15N]1
0.5 mMPDZ3[U-99% 15N]2
Sample conditionsIonic strength: PBS Not defined / Label: conditions_1 / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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