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- PDB-3h2x: Crystal Structure of The Human Lymphoid Tyrosine Phosphatase Cata... -

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Basic information

Entry
Database: PDB / ID: 3h2x
TitleCrystal Structure of The Human Lymphoid Tyrosine Phosphatase Catalytic Domain
ComponentsTyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE / SH2-like fold / Alternative splicing / Cytoplasm / Polymorphism / Protein phosphatase / Systemic lupus erythematosus
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of JUN kinase activity / 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 protein K63-linked ubiquitination ...phosphoanandamide dephosphorylation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of JUN kinase activity / 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 protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of T cell activation / negative regulation of interleukin-8 production / negative regulation of T cell receptor signaling pathway / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of NLRP3 inflammasome complex assembly / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of interleukin-6 production / T cell differentiation / negative regulation of tumor necrosis factor production / positive regulation of type I interferon production / protein-tyrosine-phosphatase / negative regulation of autophagy / protein tyrosine phosphatase activity / lipopolysaccharide-mediated signaling pathway / SH3 domain binding / lipid metabolic process / autophagy / kinase 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 / cytoplasm / cytosol
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTsai, S.J. / Sen, U.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of the human lymphoid tyrosine phosphatase catalytic domain: insights into redox regulation .
Authors: Tsai, S.J. / Sen, U. / Zhao, L. / Greenleaf, W.B. / Dasgupta, J. / Fiorillo, E. / Orru, V. / Bottini, N. / Chen, X.S.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0906
Polymers35,6151
Non-polymers4755
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.495, 68.868, 58.701
Angle α, β, γ (deg.)90.00, 101.57, 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: 35614.891 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Plasmid: pET-28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.0 M (NH4)2SO4, 0.1 M MES, 0.2 M Na/KPO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2007 / Details: Confocal
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16800 / Observed criterion σ(F): 5 / Observed criterion σ(I): 2.2 / Redundancy: 3.6 %
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.4 / % possible all: 92.6

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2CFV

2cfv


Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 15244 -Random
Rwork0.176 ---
obs0.178 16378 96.6 %-
all-16954 --
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 25 201 2722

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