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- PDB-3olr: PTPN22 in complex with consensus phospho-tyrosine peptide 1 -

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Basic information

Entry
Database: PDB / ID: 3olr
TitlePTPN22 in complex with consensus phospho-tyrosine peptide 1
Components
  • SKAP2
  • Tyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE / PTPN22 / LYP / phosphatase
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / regulation of non-canonical NF-kappaB signal transduction / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of p38MAPK cascade / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide ...phosphoanandamide dephosphorylation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / regulation of non-canonical NF-kappaB signal transduction / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of p38MAPK cascade / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of T cell activation / 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 / 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 / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of autophagy / protein tyrosine phosphatase activity / lipid metabolic process / kinase binding / autophagy / SH3 domain binding / cytoplasmic side of plasma membrane / 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: 2.5 Å
AuthorsYu, X. / Sun, J.-P. / Zhang, S. / Zhang, Z.-Y.
CitationJournal: To be Published
Title: Structure basis of LYP substrate specificity revealed by reverse alanine screening and crystallography
Authors: Yu, X. / Sun, J.P. / Chen, M. / Zhang, S. / Wang, L. / Imasaki, T. / Takagi, Y. / Zhang, Z.Y.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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
C: Tyrosine-protein phosphatase non-receptor type 22
D: Tyrosine-protein phosphatase non-receptor type 22
E: SKAP2
F: SKAP2
G: SKAP2
H: SKAP2


Theoretical massNumber of molelcules
Total (without water)151,9578
Polymers151,9578
Non-polymers00
Water7,116395
1
A: Tyrosine-protein phosphatase non-receptor type 22
E: SKAP2


Theoretical massNumber of molelcules
Total (without water)37,9892
Polymers37,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-9 kcal/mol
Surface area14390 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 22
F: SKAP2


Theoretical massNumber of molelcules
Total (without water)37,9892
Polymers37,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area14540 Å2
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 22
G: SKAP2


Theoretical massNumber of molelcules
Total (without water)37,9892
Polymers37,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area14490 Å2
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 22
H: SKAP2


Theoretical massNumber of molelcules
Total (without water)37,9892
Polymers37,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.897, 62.766, 117.461
Angle α, β, γ (deg.)99.06, 96.53, 105.06
Int Tables number1
Space group name H-MP1

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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: UNP 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
SKAP2


Mass: 1246.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence is derived from a peptide screen
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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 Å
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: 2.5→80 Å / Num. all: 41830 / Num. obs: 40826 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.5→2.59 Å / % possible all: 76.5

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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: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 3486 8.2 %RANDOM
Rwork0.1621 34551 --
obs-38037 89.1 %-
Displacement parametersBiso max: 79.23 Å2 / Biso mean: 31.5333 Å2 / Biso min: 6.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10139 0 0 395 10534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.227
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rwork0.323 --
Rfree-0 -
obs--76.49 %
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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