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- PDB-2kno: NMR Solution Structure of SH2 Domain of the Human Tensin Like C1 ... -

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Basic information

Entry
Database: PDB / ID: 2kno
TitleNMR Solution Structure of SH2 Domain of the Human Tensin Like C1 Domain Containing Phosphatase (TENC1)
ComponentsTensin-like C1 domain-containing phosphatase
KeywordsHYDROLASE / SH2 domain / TENC1 / solution structure / tensin2 / Cell junction / Cell membrane / Membrane / Metal-binding / Phorbol-ester binding / Phosphoprotein / Protein phosphatase / Zinc-finger
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 / water refine
Model detailslowest energy, model 12
AuthorsChen, L. / Feng, R. / Liu, C. / Zhu, G.
CitationJournal: To be Published
Title: NMR Solution Structure of SH2 Domain of the Human Tensin Like C1 Domain Containing Phosphatase (TENC1)
Authors: Chen, L. / Liu, C. / Feng, R. / Zhu, G.
History
DepositionAug 27, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

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MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,4031
Polymers14,4031
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 least restraint violations
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: 14402.526 Da / Num. of mol.: 1
Fragment: Src Homolog 2 domain of TENC1, UNP residues 1135-1249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: KIAA1075, TENC1, tensin like C1 domain containing phosphatase, TNS2
Plasmid: pET / Production host: Escherichia coli (E. coli)
References: UniProt: Q63HR2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1223D 1H-15N NOESY
1342D 1H-1H NOESY
1433D HNCO
1533D HN(CA)CB
1633D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 13C] SH2-1, 100mM sodium acetate-2, 100mM sodium chloride-3, 100% D2O100% D2O
21mM [U-100% 15N] SH2-4, 100mM sodium acetate-5, 100mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
31mM [U-100% 13C; U-100% 15N] SH2-7, 100mM sodium acetate-8, 100mM sodium chloride-9, 90% H2O/10% D2O90% H2O/10% D2O
41mM SH2-10, 100mM sodium acetate-11, 100mM sodium chloride-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSH2-1[U-100% 13C]1
100 mMsodium acetate-21
100 mMsodium chloride-31
1 mMSH2-4[U-100% 15N]2
100 mMsodium acetate-52
100 mMsodium chloride-62
1 mMSH2-7[U-100% 13C; U-100% 15N]3
100 mMsodium acetate-83
100 mMsodium chloride-93
1 mMSH2-104
100 mMsodium acetate-114
100 mMsodium chloride-124
Sample conditionsIonic strength: 100mM / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger A. T. et.al.structure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
SPARKYGoddarddata analysis
CYANAGuntert, Mumenthaler, Wuthrichstructure solution
RefinementMethod: water refine / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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