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- PDB-2qcj: Native Structure of Lyp -

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Basic information

Entry
Database: PDB / ID: 2qcj
TitleNative Structure of Lyp
ComponentsTyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE / PTPN22 / LYP / PTP
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSun, J.P. / Yu, X. / Zhang, Z.Y.
CitationJournal: To be Published
Title: Crystal structure of Lyp and its complex with a selective inhibitor
Authors: Yu, X. / Sun, J.P. / He, Y.T. / Zhou, B. / Liu, S.J. / Zhang, Z.Y.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)73,5182
Polymers73,5182
Non-polymers00
Water41423
1
A: Tyrosine-protein phosphatase non-receptor type 22


Theoretical massNumber of molelcules
Total (without water)36,7591
Polymers36,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 22


Theoretical massNumber of molelcules
Total (without water)36,7591
Polymers36,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.309, 93.953, 148.173
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: 36759.129 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: 20% PEG 3350, pH 5.6, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 20, 2005
RadiationMonochromator: GRAPHITE / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 13575 / Num. obs: 12511 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Rsym value: 0.141 / Net I/σ(I): 15.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1151 / Rsym value: 0.635 / % possible all: 86.67

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PXH

1pxh


Resolution: 3→50 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 990 -random
Rwork0.284 ---
all0.287 13575 --
obs0.287 12511 92.2 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 0 23 4631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0095
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_angle_d1.62
X-RAY DIFFRACTIONx_improper_angle_d0.97
LS refinement shell
Highest resolution (Å)Refine-ID
3X-RAY DIFFRACTION
3.11X-RAY DIFFRACTION
3.23X-RAY DIFFRACTION
3.38X-RAY DIFFRACTION
3.56X-RAY DIFFRACTION
3.78X-RAY DIFFRACTION

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