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- PDB-2m10: trans form of a photoswitchable PDZ domain crosslinked with an az... -

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Basic information

Entry
Database: PDB / ID: 2m10
Titletrans form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative
ComponentsTyrosine-protein phosphatase non-receptor type 13
KeywordsHYDROLASE / photoswitch
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 / cytoplasm / cytosol
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
Chem-33B / Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsWalser, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Kinetic response of a photoperturbed allosteric protein.
Authors: Buchli, B. / Waldauer, S.A. / Walser, R. / Donten, M.L. / Pfister, R. / Blochliger, N. / Steiner, S. / Caflisch, A. / Zerbe, O. / Hamm, P.
History
DepositionNov 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5932
Polymers10,0671
Non-polymers5251
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 13 / Fas-associated protein-tyrosine phosphatase 1 / FAP-1 / PTP-BAS / Protein-tyrosine phosphatase 1E / ...Fas-associated protein-tyrosine phosphatase 1 / FAP-1 / PTP-BAS / Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / Protein-tyrosine phosphatase PTPL1


Mass: 10067.399 Da / Num. of mol.: 1 / Fragment: PDZ 2 domain residues 1361-1456 / Mutation: S1381C, E1436C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN13, PNP1, PTP1E, PTPL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q12923, protein-tyrosine-phosphatase
#2: Chemical ChemComp-33B / 3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid}


Mass: 525.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14Cl2N4O8S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1232D 1H-13C HSQC aliphatic
1332D 1H-13C HSQC aromatic
1433D CBCA(CO)NH
1533D HNCO
1633D HN(CA)CB
1733D (H)CCH-TOCSY
1833D C(CO)NH
1933D 1H-15N NOESY
11033D 1H-13C NOESY aliphatic
11122D 1H-15N HSQC
11212D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 4.3 % C12E5, 1.8 % n-hexanol, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM [U-100% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 8.5 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
30.75 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMentity_1-1[U-100% 15N]1
50 mMsodium phosphate-21
150 mMsodium chloride-31
0.1 mMsodium azide-41
4.3 %C12E5-51
1.8 %n-hexanol-61
0.75 mMentity_1-7[U-100% 15N]2
50 mMsodium phosphate-82
150 mMsodium chloride-92
0.1 mMsodium azide-102
8.5 mg/mLPf1 phage-112
0.75 mMentity_1-12[U-99% 13C; U-99% 15N]3
50 mMsodium phosphate-133
150 mMsodium chloride-143
0.1 mMsodium azide-153
Sample conditionsIonic strength: 0.2 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.9.0b3Keller and Wuthrichchemical shift assignment
TALOS3.80F1 Rev 2012.080.14.41Cornilescu, Delaglio and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckNMRLaskowski and MacArthurdata analysis
WHAT IFVrienddata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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