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- PDB-1q7x: Solution structure of the alternatively spliced PDZ2 domain (PDZ2... -

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Basic information

Entry
Database: PDB / ID: 1q7x
TitleSolution structure of the alternatively spliced PDZ2 domain (PDZ2b) of PTP-Bas (hPTP1E)
ComponentsPDZ2b domain of PTP-Bas (hPTP1E)
KeywordsHYDROLASE / Phosphatase / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation ...negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / fibrillar center / lamellipodium / cell body / cytoskeleton / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / 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 / FERM N-terminal domain ...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 / PDZ domain / Pdz3 Domain / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKachel, N. / Erdmann, K.S. / Kremer, W. / Wolff, P. / Gronwald, W. / Heumann, R. / Kalbitzer, H.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): Splicing induced modulation of ligand specificity.
Authors: Kachel, N. / Erdmann, K.S. / Kremer, W. / Wolff, P. / Gronwald, W. / Heumann, R. / Kalbitzer, H.R.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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: PDZ2b domain of PTP-Bas (hPTP1E)


Theoretical massNumber of molelcules
Total (without water)11,2981
Polymers11,2981
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PDZ2b domain of PTP-Bas (hPTP1E)


Mass: 11297.679 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP1E / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q12923

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM PDZ2b U-15N, 13C; 50mM phosphate buffer with 150mM sodium chloride92% H20, 8% D2O
22mM PDZ2b U-15N; 50mM phosphate buffer with 150mM sodium chloride92% H20, 8% D2O
32mM PDZ2b unlabeled; 50mM phosphate buffer with 150mM sodium chloride92% H20, 8% D2O
Sample conditionsIonic strength: 50mM sodium phosphate, 150mM sodium chloride
pH: 6.8 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
XwinNMR2.6Bruker Biospinprocessing
AUREMOL1.1Gronwald et aldata analysis
CNS1.1Brunger et alstructure solution
CNS1.1Brunger et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 1648 NOE-derived distance restraints and 80 torsion angle restraints acquired by TALOS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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