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- PDB-2p6x: Crystal structure of human tyrosine phosphatase PTPN22 -

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Basic information

Entry
Database: PDB / ID: 2p6x
TitleCrystal structure of human tyrosine phosphatase PTPN22
ComponentsTyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE / Tyrosine phosphatase / Lymphoid phosphatase / PEP / LYP / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway ...phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of T cell activation / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of interleukin-8 production / negative regulation of JUN kinase activity / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of CD8-positive, alpha-beta T cell proliferation / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / negative regulation of interleukin-6 production / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / T cell differentiation / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / protein dephosphorylation / negative regulation of autophagy / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / lipid metabolic process / cytoplasmic side of plasma membrane / autophagy / kinase binding / SH3 domain binding / positive regulation of type II interferon production / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Non-receptor tyrosine-protein phosphatase 22 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...: / Non-receptor tyrosine-protein phosphatase 22 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUgochukwu, E. / Salah, E. / Barr, A. / Shrestha, L. / Alfano, I. / Burgess-Brown, N. / King, O. / Umeano, C. / Papagrigoriou, E. / Pike, A.C.W. ...Ugochukwu, E. / Salah, E. / Barr, A. / Shrestha, L. / Alfano, I. / Burgess-Brown, N. / King, O. / Umeano, C. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Turnbull, A. / Uppenberg, J. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 22
B: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3137
Polymers73,0302
Non-polymers2845
Water6,648369
1
A: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7014
Polymers36,5151
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6123
Polymers36,5151
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.961, 48.442, 119.805
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 3 - 298 / Label seq-ID: 3 - 298

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 22 / Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP


Mass: 36514.840 Da / Num. of mol.: 2
Fragment: PTPN22, Tyrosine-protein phosphatase catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 100 mM Bicine pH 7.9, 25% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→59.44 Å / Num. all: 54178 / Num. obs: 54178 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.389 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OC3

2oc3


Resolution: 1.9→59.44 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.611 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21725 2761 5.1 %RANDOM
Rwork0.16352 ---
all0.16627 51408 --
obs0.16627 51408 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.41 Å2
2--0.5 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→59.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 17 369 5216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224983
X-RAY DIFFRACTIONr_bond_other_d0.0010.023440
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9616750
X-RAY DIFFRACTIONr_angle_other_deg0.94138376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78423.938226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1621530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
X-RAY DIFFRACTIONr_nbd_refined0.2130.2979
X-RAY DIFFRACTIONr_nbd_other0.2060.23458
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22461
X-RAY DIFFRACTIONr_nbtor_other0.0870.22580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.221
X-RAY DIFFRACTIONr_mcbond_it5.09853160
X-RAY DIFFRACTIONr_mcbond_other2.41451194
X-RAY DIFFRACTIONr_mcangle_it5.95674898
X-RAY DIFFRACTIONr_scbond_it8.34692210
X-RAY DIFFRACTIONr_scangle_it9.561111846
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1740medium positional0.430.5
2231loose positional0.585
1740medium thermal1.752
2231loose thermal2.9710
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 221 -
Rwork0.211 3746 -
obs--99.85 %
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)
11.27850.0675-0.09570.6731-0.10811.0419-0.030.08190.1169-0.05790.04570.09040.0209-0.0415-0.0157-0.1113-0.0074-0.0198-0.12360.0215-0.076425.593420.5471103.5649
21.2182-0.0661-0.07631.3803-0.63171.9396-0.06290.17470.0031-0.2246-0.0545-0.1570.1370.18490.1174-0.06570.01470.023-0.08730.0001-0.1232-2.533821.204170.5653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3031 - 303
2X-RAY DIFFRACTION2BB3 - 2983 - 298

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