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- PDB-2l6k: Solution Structure of a Nonphosphorylated Peptide Recognizing Domain -

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Basic information

Entry
Database: PDB / ID: 2l6k
TitleSolution Structure of a Nonphosphorylated Peptide Recognizing Domain
ComponentsTensin-like C1 domain-containing phosphatase
KeywordsPROTEIN BINDING / ANTITUMOR PROTEIN / CELL ADHESION
Function / homology
Function and homology information


multicellular organismal-level homeostasis / collagen metabolic process / cellular homeostasis / response to muscle activity / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / protein-tyrosine-phosphatase / kidney development / protein tyrosine phosphatase activity / multicellular organism growth ...multicellular organismal-level homeostasis / collagen metabolic process / cellular homeostasis / response to muscle activity / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / protein-tyrosine-phosphatase / kidney development / protein tyrosine phosphatase activity / multicellular organism growth / kinase binding / negative regulation of cell population proliferation / focal adhesion / lipid binding / identical protein binding / metal ion binding / plasma membrane / 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 / Phorbol esters/diacylglycerol binding domain (C1 domain) / SH2 domain / SHC Adaptor Protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsDai, K. / Liao, S. / Zhang, J. / Zhang, X. / Tu, X.
CitationJournal: Plos One / Year: 2011
Title: Solution structure of Tensin2 SH2 domain and its phosphotyrosine-independent interaction with DLC-1
Authors: Dai, K. / Liao, S. / Zhang, J. / Zhang, X. / Tu, X.
History
DepositionNov 22, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tensin-like C1 domain-containing phosphatase


Theoretical massNumber of molelcules
Total (without water)13,6881
Polymers13,6881
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 Tensin-like C1 domain-containing phosphatase / C1 domain-containing phosphatase and tensin homolog / C1-TEN / Tensin-2


Mass: 13687.777 Da / Num. of mol.: 1
Fragment: Nonphosphorylated Peptide Recognizing Domain, SH2 domain, UNP residues 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q63HR2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D C(CO)NH
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D HN(CO)CA
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.6mM [U-99% 13C; U-99% 15N] Protein Domain; 150mM sodium chloride; 20mM sodium phosphate; 2mM EDTA; 50mM Arginine; 50mM glutamine; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMProtein Domain-1[U-99% 13C; U-99% 15N]1
150 mMsodium chloride-21
20 mMsodium phosphate-31
2 mMEDTA-41
50 mMArginine-51
50 mMglutamine-61
Sample conditionsIonic strength: 150 / pH: 6.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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