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- PDB-3omh: Crystal structure of PTPN22 in complex with SKAP-HOM pTyr75 peptide -

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Basic information

Entry
Database: PDB / ID: 3omh
TitleCrystal structure of PTPN22 in complex with SKAP-HOM pTyr75 peptide
Components
  • Src kinase-associated phosphoprotein 2
  • Tyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE / tyrosine phosphatase
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 / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 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 / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / 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 / Signal regulatory protein family interactions / 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 / B cell activation / 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 / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / T cell differentiation / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / negative regulation of autophagy / protein dephosphorylation / 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 / protein-containing complex assembly / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SKAP family / : / 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 ...SKAP family / : / 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. / PH domain / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Src kinase-associated phosphoprotein 2 / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYu, X. / Sun, J.-P. / Zhang, S. / Zhang, Z.-Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Substrate Specificity of Lymphoid-specific Tyrosine Phosphatase (Lyp) and Identification of Src Kinase-associated Protein of 55 kDa Homolog (SKAP-HOM) as a Lyp Substrate.
Authors: Yu, X. / Chen, M. / Zhang, S. / Yu, Z.H. / Sun, J.P. / Wang, L. / Liu, S. / Imasaki, T. / Takagi, Y. / Zhang, Z.Y.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 22
B: Tyrosine-protein phosphatase non-receptor type 22
C: Tyrosine-protein phosphatase non-receptor type 22
D: Tyrosine-protein phosphatase non-receptor type 22
E: Src kinase-associated phosphoprotein 2
F: Src kinase-associated phosphoprotein 2
G: Src kinase-associated phosphoprotein 2
H: Src kinase-associated phosphoprotein 2


Theoretical massNumber of molelcules
Total (without water)151,6368
Polymers151,6368
Non-polymers00
Water2,522140
1
A: Tyrosine-protein phosphatase non-receptor type 22
E: Src kinase-associated phosphoprotein 2


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,9092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-9 kcal/mol
Surface area14110 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 22
F: Src kinase-associated phosphoprotein 2


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,9092
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-10 kcal/mol
Surface area14150 Å2
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 22
G: Src kinase-associated phosphoprotein 2


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,9092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-10 kcal/mol
Surface area13960 Å2
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 22
H: Src kinase-associated phosphoprotein 2


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,9092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-11 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.229, 46.707, 121.493
Angle α, β, γ (deg.)90.00, 101.43, 90.00
Int Tables number4
Space group name H-MP1211

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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: 36743.066 Da / Num. of mol.: 4
Fragment: Tyrosine-protein phosphatase domain residues 1-294
Mutation: C227S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#2: Protein/peptide
Src kinase-associated phosphoprotein 2 / Src family-associated phosphoprotein 2 / Src kinase-associated phosphoprotein 55-related protein / ...Src family-associated phosphoprotein 2 / Src kinase-associated phosphoprotein 55-related protein / SKAP55 homolog / SKAP-55HOM / SKAP-HOM / Src-associated adapter protein with PH and SH3 domains / Pyk2/RAFTK-associated protein / Retinoic acid-induced protein 70


Mass: 1165.999 Da / Num. of mol.: 4 / Fragment: sequence database residues 71-79 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: O75563
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / pH: 7
Details: 20% PEG 3350, 0.1M Tris-Hcl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 17, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.898→80 Å / Num. obs: 33348 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.898→3 Å / % possible all: 74

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
CNS1.1refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→36.752 Å / Cor.coef. Fo:Fc: 0.921 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 2272 RANDOM
Rwork0.229 --
obs0.231 27209 -
all-26068 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.555 Å20 Å217.819 Å2
2--8.008 Å20 Å2
3----5.454 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.9→36.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10015 0 0 140 10155
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4741.5
X-RAY DIFFRACTIONc_mcangle_it2.1532
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.11 Å /
RfactorNum. reflection
Rfree0.339 187
Rwork0.327 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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