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- PDB-1ozi: The alternatively spliced PDZ2 domain of PTP-BL -

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Basic information

Entry
Database: PDB / ID: 1ozi
TitleThe alternatively spliced PDZ2 domain of PTP-BL
Componentsprotein tyrosine phosphatase
KeywordsHYDROLASE / all-beta protein / PDZ domain / interaction with C-termini / APC / Adenomatous Polyposis Coli / RIL / reversion induced LIM
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 / PDZ domain / Pdz3 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / cartesian space distance geometry, restrained molecular dynamics
AuthorsWalma, T. / Aelen, J. / Oostendorp, M. / van den Berk, L. / Hendriks, W. / Vuister, G.W.
CitationJournal: Structure / Year: 2004
Title: A Closed Binding Pocket and Global Destabilization Modify the Binding Properties of an Alternatively Spliced Form of the Second PDZ Domain of PTP-BL.
Authors: Walma, T. / Aelen, J. / Nabuurs, S.B. / Oostendorp, M. / van den Berk, L. / Hendriks, W. / Vuister, G.W.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein tyrosine phosphatase


Theoretical massNumber of molelcules
Total (without water)10,3711
Polymers10,3711
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)30 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein protein tyrosine phosphatase / NONRECEPTOR-TYPE / 13 / PROTEIN-TYROSINE PHOSPHATASE RIP / PHOSPHOPROTEIN PHOSPHATASE / PROTEIN- ...NONRECEPTOR-TYPE / 13 / PROTEIN-TYROSINE PHOSPHATASE RIP / PHOSPHOPROTEIN PHOSPHATASE / PROTEIN-TYROSINE-PHOSPHATASE / PHOSPHOTYROSINE PHOSPHATASE / PTPASE / PTP36 / BAS-LIKE


Mass: 10370.792 Da / Num. of mol.: 1 / Fragment: PDZ2 of PTP-BL / Mutation: INS (VLFDK-G36)
Source method: isolated from a genetically manipulated source
Details: Longer alternative splice variant / Source: (gene. exp.) Mus musculus (house mouse) / Gene: PTP-BL / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli)
Strain (production host): Escherichia coli BL21 Codon Plus (DE3) RIL competent
References: UniProt: Q64512, protein-tyrosine-phosphatase

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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
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.4mM PDZ2_AS, 13C/15N labelled, 50mM potassium phosphate buffer, 50mM KCl
Solvent system: 95% H20, 5% D20
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio et al.processing
X-PLOR3.851Brungerrefinement
X-PLORNIHBrunger, NIHrefinement
RefinementMethod: cartesian space distance geometry, restrained molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 1459 restraints: 1354 are NOE-derived distance constraints, 76 dihedral angle restraints, 29 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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