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- PDB-9c54: Crystal structure of human PTPN2 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 9c54
TitleCrystal structure of human PTPN2 catalytic domain
ComponentsTyrosine-protein phosphatase non-receptor type 2
KeywordsHYDROLASE / phosphatase / apo
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 type I interferon-mediated signaling pathway / negative regulation of T cell receptor 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 / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of lipid storage / T cell differentiation / non-membrane spanning protein tyrosine phosphatase activity / 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 / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / 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 / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / 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. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / 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: 2.05 Å
AuthorsBester, S.M. / Linwood, R. / Wu, W.-I. / Mou, T.-C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Enhancing the apo protein tyrosine phosphatase non-receptor type 2 crystal soaking strategy through inhibitor-accessible binding sites.
Authors: Bester, S.M. / Linwood, R. / Kataoka, R. / Wu, W.I. / Mou, T.C.
History
DepositionJun 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 25, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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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


Theoretical massNumber of molelcules
Total (without water)36,7161
Polymers36,7161
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.742, 223.058, 36.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 36715.621 Da / Num. of mol.: 1
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.: 205 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% w/v PEG 8000, 14% v/v ethylene glycol, 25mM sodium l-glutamate, 25mM dl-alanine, 25mM glycine, 25mM dl-lysine HCl, 25mM dl-serine, 100mM MES/imidazole pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→55.6 Å / Num. obs: 22095 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.91 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.072 / Net I/σ(I): 15.1
Reflection shellResolution: 2.05→2.13 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3164 / CC1/2: 0.917 / Rpim(I) all: 0.329 / Rrim(I) all: 0.632 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→39.37 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1095 4.96 %
Rwork0.1864 20976 -
obs0.1887 22071 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.27 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 0 205 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312420
X-RAY DIFFRACTIONf_angle_d0.58353286
X-RAY DIFFRACTIONf_chiral_restr0.048355
X-RAY DIFFRACTIONf_plane_restr0.0045427
X-RAY DIFFRACTIONf_dihedral_angle_d15.3074901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.140.30931360.23332570X-RAY DIFFRACTION99.96
2.14-2.260.2651400.21152556X-RAY DIFFRACTION99.93
2.26-2.40.27721460.21542572X-RAY DIFFRACTION99.93
2.4-2.580.27511300.21292600X-RAY DIFFRACTION99.82
2.58-2.840.25331420.21052597X-RAY DIFFRACTION100
2.84-3.260.28831170.20052638X-RAY DIFFRACTION99.96
3.26-4.10.20051470.16312657X-RAY DIFFRACTION100
4.1-39.370.20961370.1722786X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.80353422522-2.714463917812.656911867863.481862533410.0001236050298286.161900978050.3738124086680.439100886308-1.05102130071-0.5832969110370.06772039737630.614677963941.00569921504-0.271761890948-0.5040440323830.430933526394-0.152185589623-0.1176380973680.499204955878-0.05932521183170.77553587277210.092437511213.1372890221-10.3541197948
24.736936961330.8990769885190.3665165182778.56684079116-0.8102737621141.22392788127-0.2403396091290.1910804987970.214688554925-0.177304401860.4126142315720.760367035508-0.123636294888-0.266307882583-0.2009483539430.32204478120.0660373981661-0.07668903683740.3974538457610.07489267199580.38319745213411.801470920844.3448515622-11.9878007334
35.64271267578-1.401322173590.9511634269452.340251881610.05727146664852.66674359224-0.259723004250.04295604314570.2079978776690.1948596320790.121473028286-0.0410177671154-0.156974637695-0.02490070450510.1312883489620.2966008729230.0272969627122-0.07541402005160.236799271022-0.005386152364670.25255745910226.609898996240.6572793171-4.13074184819
44.00399184678-0.03799774771491.420217856895.41148270521-0.08732970693181.6826959926-0.0609182155698-0.253667609238-0.2048581359680.5206460589080.1186574122910.0457769360418-0.0263541713299-0.202494470723-0.06725765358560.2951465843490.0726732099073-0.0371591363390.304716401922-0.05635154025190.25061253544328.285790018329.52475764250.84049467991
56.43811635962-1.502449635362.597054881429.08480635941-0.7454380589113.568507655150.128249498242-0.071653469328-1.010971799350.2320267151760.228323774850.6134012496520.349144889176-0.336103298338-0.3424348529940.24497199989-0.0510661788709-0.05150227431080.339903977079-0.02966550581280.48176390955214.363140902821.5065596675-4.7062838421
67.434008380840.106327217905-4.654311196762.00821271275-0.09639676904799.872678988920.390587901071-0.946322288092-1.691841557350.4433783125470.154910268712-0.4263110580860.8076129368420.657866222387-0.4816379263870.8799763172460.0940695373649-0.1860864364490.8797414827760.03122413520481.1449823870233.753619756214.1543894032.93871523756
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 27 )2 - 271 - 26
22chain 'A' and (resid 28 through 45 )28 - 4527 - 44
33chain 'A' and (resid 46 through 150 )46 - 15045 - 149
44chain 'A' and (resid 151 through 237 )151 - 237150 - 236
55chain 'A' and (resid 238 through 277 )238 - 277237 - 274
66chain 'A' and (resid 278 through 296 )278 - 296275 - 287

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