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- PDB-7f5o: Crystal structure of PTPN2 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 7f5o
TitleCrystal structure of PTPN2 catalytic domain
ComponentsTyrosine-protein phosphatase non-receptor type 2
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / TCPTP / PTPN2
Function / homology
Function and homology information


negative regulation of interleukin-2-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / negative regulation of macrophage differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of chemotaxis ...negative regulation of interleukin-2-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / negative regulation of macrophage differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of chemotaxis / negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / Interleukin-37 signaling / syntaxin binding / negative regulation of T cell receptor signaling pathway / negative regulation of type I interferon-mediated signaling pathway / STAT family protein binding / regulation of hepatocyte growth factor receptor signaling pathway / insulin receptor recycling / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of type II interferon-mediated signaling pathway / negative regulation of lipid storage / non-membrane spanning protein tyrosine phosphatase activity / endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation / peptidyl-tyrosine dephosphorylation / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of IFNG signaling / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / B cell differentiation / protein-tyrosine-phosphatase / erythrocyte differentiation / protein tyrosine phosphatase activity / endosome lumen / PKR-mediated signaling / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / negative regulation of inflammatory response / integrin binding / insulin receptor signaling pathway / glucose homeostasis / negative regulation of cell population proliferation / protein kinase binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / 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 active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain ...Protein-tyrosine phosphatase, non-receptor type-1/2 / 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 active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
IODIDE ION / Tyrosine-protein phosphatase non-receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSingh, J.P. / Lin, M.-J. / Hsu, S.-F. / Lee, C.-C. / Meng, T.-C.
CitationJournal: Biochemistry / Year: 2021
Title: Crystal Structure of TCPTP Unravels an Allosteric Regulatory Role of Helix alpha 7 in Phosphatase Activity.
Authors: Singh, J.P. / Lin, M.J. / Hsu, S.F. / Peti, W. / Lee, C.C. / Meng, T.C.
History
DepositionJun 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 2
B: Tyrosine-protein phosphatase non-receptor type 2
C: Tyrosine-protein phosphatase non-receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2149
Polymers106,4533
Non-polymers7616
Water9,962553
1
A: Tyrosine-protein phosphatase non-receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8654
Polymers35,4841
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6112
Polymers35,4841
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase non-receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7383
Polymers35,4841
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.094, 68.187, 72.683
Angle α, β, γ (deg.)111.540, 102.659, 92.337
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 2 / T-cell protein-tyrosine phosphatase / TCPTP


Mass: 35484.184 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN2, PTPT / Production host: Escherichia coli (E. coli) / References: UniProt: P17706, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris Propane (pH-7.5), 0.2 M Sodium Iodide, 20% w/v PEG 3350, 10% v/v Ethylene glycol and 0.9 mM Mitoxantrone additive

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Data collection

DiffractionMean temperature: 107 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 100918 / % possible obs: 96.4 % / Redundancy: 2.5 % / CC1/2: 0.98 / CC star: 0.99 / Rmerge(I) obs: 0.022 / Net I/σ(I): 33.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 10037 / CC1/2: 0.92 / CC star: 0.98 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8K

1l8k


Resolution: 1.7→24.848 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.2 / SU B: 2.346 / SU ML: 0.078 / Average fsc free: 0.9123 / Average fsc work: 0.9237 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.241 4866 4.842 %
Rwork0.1989 95640 -
all0.201 --
obs-100506 95.952 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.062 Å20.131 Å20.056 Å2
2---0.04 Å20.022 Å2
3---0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 6 553 7514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137123
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176464
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6489644
X-RAY DIFFRACTIONr_angle_other_deg1.3951.57415016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26921.939423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42151252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3151556
X-RAY DIFFRACTIONr_chiral_restr0.0850.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021561
X-RAY DIFFRACTIONr_nbd_refined0.2180.21393
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26117
X-RAY DIFFRACTIONr_nbtor_refined0.170.23448
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2433
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3790.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.218
X-RAY DIFFRACTIONr_nbd_other0.1920.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.230
X-RAY DIFFRACTIONr_mcbond_it1.8481.863372
X-RAY DIFFRACTIONr_mcbond_other1.8451.8593371
X-RAY DIFFRACTIONr_mcangle_it2.7712.7754201
X-RAY DIFFRACTIONr_mcangle_other2.7712.7764202
X-RAY DIFFRACTIONr_scbond_it2.4162.173751
X-RAY DIFFRACTIONr_scbond_other2.412.1683749
X-RAY DIFFRACTIONr_scangle_it3.8243.1365443
X-RAY DIFFRACTIONr_scangle_other3.8193.1365443
X-RAY DIFFRACTIONr_lrange_it5.51222.3528147
X-RAY DIFFRACTIONr_lrange_other5.42122.1818037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.2863220.2456676X-RAY DIFFRACTION90.3434
1.744-1.7910.2613470.2336836X-RAY DIFFRACTION95.4171
1.791-1.8430.2763380.2236664X-RAY DIFFRACTION95.7342
1.843-1.90.2353520.2086452X-RAY DIFFRACTION95.6558
1.9-1.9610.2442930.2166261X-RAY DIFFRACTION95.6649
1.961-2.030.2452860.2066102X-RAY DIFFRACTION95.7865
2.03-2.1060.2513110.2065750X-RAY DIFFRACTION95.0596
2.106-2.1910.2573150.2085677X-RAY DIFFRACTION95.673
2.191-2.2880.2442870.1955364X-RAY DIFFRACTION95.9912
2.288-2.3990.242740.1985195X-RAY DIFFRACTION96.1329
2.399-2.5270.2382530.1884983X-RAY DIFFRACTION96.6587
2.527-2.6790.2252200.1894726X-RAY DIFFRACTION96.9614
2.679-2.8610.2312370.1944443X-RAY DIFFRACTION97.3985
2.861-3.0870.2282170.1924160X-RAY DIFFRACTION97.9195
3.087-3.3770.2241800.1943870X-RAY DIFFRACTION98.3487
3.377-3.7670.2361630.1943525X-RAY DIFFRACTION98.821
3.767-4.3330.2321620.1743103X-RAY DIFFRACTION98.8795
4.333-5.2670.231430.1682618X-RAY DIFFRACTION98.5016
5.267-7.2890.2461080.2172053X-RAY DIFFRACTION98.4062
7.289-24.840.255570.2121174X-RAY DIFFRACTION95.2049

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