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- PDB-7f5n: Crystal structure of TCPTP catalytic domain -

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Basic information

Entry
Database: PDB / ID: 7f5n
TitleCrystal structure of TCPTP 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 positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of interleukin-4-mediated signaling pathway / 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 / regulation of type II interferon-mediated signaling pathway / negative regulation of macrophage differentiation / negative regulation of tyrosine phosphorylation of STAT protein ...negative regulation of interleukin-2-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of interleukin-4-mediated signaling pathway / 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 / regulation of type II interferon-mediated signaling pathway / negative regulation of macrophage differentiation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of chemotaxis / 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 type I interferon-mediated signaling pathway / regulation of hepatocyte growth factor receptor signaling pathway / insulin receptor recycling / STAT family protein binding / negative regulation of T cell receptor signaling pathway / negative regulation of type II interferon-mediated signaling pathway / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of epidermal growth factor receptor signaling pathway / peptidyl-tyrosine dephosphorylation / negative regulation of lipid storage / non-membrane spanning protein tyrosine phosphatase activity / T cell differentiation / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of IFNG signaling / positive regulation of gluconeogenesis / protein-tyrosine-phosphatase / negative regulation of insulin receptor signaling pathway / B cell differentiation / protein tyrosine phosphatase activity / erythrocyte differentiation / endosome lumen / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / PKR-mediated signaling / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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 ...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
Tyrosine-protein phosphatase non-receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 1.1Feb 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 1.2Nov 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


Theoretical massNumber of molelcules
Total (without water)110,7923
Polymers110,7923
Non-polymers00
Water7,386410
1
A: Tyrosine-protein phosphatase non-receptor type 2


Theoretical massNumber of molelcules
Total (without water)36,9311
Polymers36,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 2


Theoretical massNumber of molelcules
Total (without water)36,9311
Polymers36,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase non-receptor type 2


Theoretical massNumber of molelcules
Total (without water)36,9311
Polymers36,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.570, 68.056, 73.244
Angle α, β, γ (deg.)112.932, 106.459, 92.459
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: 36930.824 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.15 M Ammonium nitrate, 0.1 M MES (pH-6.0), 20% v/v PEG smear medium, 5% v/v Ethylene glycol and 5.5 mM lysine dipeptide 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: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 63299 / % possible obs: 92 % / Redundancy: 2.2 % / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.017 / Net I/σ(I): 41.6
Reflection shellResolution: 1.93→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 9.7 / Num. unique obs: 6637 / CC1/2: 0.98 / CC star: 0.99 / % possible all: 96.3

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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: 1.93→19.948 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.572 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2376 3120 4.966 %
Rwork0.1834 59707 -
all0.186 --
obs-62827 91.178 %
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: 24.787 Å2
Baniso -1Baniso -2Baniso -3
1--0.153 Å20.09 Å20.072 Å2
2---0.064 Å20.017 Å2
3---0.087 Å2
Refinement stepCycle: LAST / Resolution: 1.93→19.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7191 0 0 410 7601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176700
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6479955
X-RAY DIFFRACTIONr_angle_other_deg1.3531.57615577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82222.069435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.566151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.11557
X-RAY DIFFRACTIONr_chiral_restr0.0850.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021598
X-RAY DIFFRACTIONr_nbd_refined0.2070.21446
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.26460
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.23413
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2342
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.231
X-RAY DIFFRACTIONr_nbd_other0.2760.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.223
X-RAY DIFFRACTIONr_mcbond_it2.2022.4343489
X-RAY DIFFRACTIONr_mcbond_other2.22.4333488
X-RAY DIFFRACTIONr_mcangle_it3.2963.6284349
X-RAY DIFFRACTIONr_mcangle_other3.2963.634350
X-RAY DIFFRACTIONr_scbond_it2.6492.783871
X-RAY DIFFRACTIONr_scbond_other2.6482.7823872
X-RAY DIFFRACTIONr_scangle_it4.2254.0275606
X-RAY DIFFRACTIONr_scangle_other4.2244.0285607
X-RAY DIFFRACTIONr_lrange_it6.02428.088317
X-RAY DIFFRACTIONr_lrange_other5.96628.0098246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.2382110.1964249X-RAY DIFFRACTION88.3868
1.98-2.0340.242330.1954465X-RAY DIFFRACTION94.9091
2.034-2.0920.2332000.1934415X-RAY DIFFRACTION96.852
2.092-2.1560.2292380.1884243X-RAY DIFFRACTION96.5733
2.156-2.2260.2442170.194040X-RAY DIFFRACTION93.8078
2.226-2.3030.3071350.2672483X-RAY DIFFRACTION59.5677
2.303-2.3880.2381970.1723846X-RAY DIFFRACTION97.1875
2.388-2.4840.2571990.1763743X-RAY DIFFRACTION96.7837
2.484-2.5930.2572040.1833594X-RAY DIFFRACTION96.9372
2.593-2.7170.2571940.193368X-RAY DIFFRACTION96.1144
2.717-2.8610.2751800.1893224X-RAY DIFFRACTION95.6986
2.861-3.0310.2351500.1853004X-RAY DIFFRACTION94.1493
3.031-3.2350.2421650.1882805X-RAY DIFFRACTION93.3962
3.235-3.4870.2261200.1882504X-RAY DIFFRACTION90.2028
3.487-3.8080.228990.1772026X-RAY DIFFRACTION78.0676
3.808-4.2380.22930.1681946X-RAY DIFFRACTION82.0523
4.238-4.8580.19900.1481927X-RAY DIFFRACTION92.4805
4.858-5.8640.225770.1651676X-RAY DIFFRACTION95.3235
5.864-7.9570.197850.1671387X-RAY DIFFRACTION98.33
7.957-19.940.255330.205762X-RAY DIFFRACTION86.6013

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