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- PDB-7c8s: Crystal structure of DUSP22 mutant_N128A -

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Basic information

Entry
Database: PDB / ID: 7c8s
TitleCrystal structure of DUSP22 mutant_N128A
ComponentsDual specificity protein phosphatase 22
KeywordsHYDROLASE / DUSP22 / atypical DUSPs / Cysteine based protein tyrosine phosphatases (Cys-based PTPs) / active site of DUSPs
Function / homology
Function and homology information


negative regulation of T cell mediated immunity / leading edge of lamellipodium / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell activation / protein tyrosine kinase inhibitor activity / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / filamentous actin / protein serine/threonine phosphatase activity ...negative regulation of T cell mediated immunity / leading edge of lamellipodium / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell activation / protein tyrosine kinase inhibitor activity / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / filamentous actin / protein serine/threonine phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / immune system process / protein-tyrosine-phosphatase / transforming growth factor beta receptor signaling pathway / protein tyrosine phosphatase activity / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / positive regulation of JNK cascade / regulation of cell population proliferation / intracellular signal transduction / negative regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Dual specificity protein phosphatase 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.31 Å
AuthorsLai, C.H. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases.
Authors: Lai, C.H. / Chang, C.C. / Chuang, H.C. / Tan, T.H. / Lyu, P.C.
History
DepositionJun 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8642
Polymers17,7681
Non-polymers961
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.842, 50.432, 40.212
Angle α, β, γ (deg.)90.000, 95.960, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Dual specificity protein phosphatase 22 / JNK-stimulatory phosphatase-1 / JSP-1 / Low molecular weight dual specificity phosphatase 2 / LMW- ...JNK-stimulatory phosphatase-1 / JSP-1 / Low molecular weight dual specificity phosphatase 2 / LMW-DSP2 / Mitogen-activated protein kinase phosphatase x / MKP-x


Mass: 17768.357 Da / Num. of mol.: 1 / Mutation: N128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP22, JSP1, LMWDSP2, MKPX / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRW4, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 30% PEG 3,350, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→30 Å / Num. obs: 42476 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.13 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.31-1.363.70.64541840.7190.3880.7551.01797.4
1.36-1.413.70.52441760.8090.3150.6131.01497.9
1.41-1.483.70.35642030.8890.2130.4161.00498.1
1.48-1.553.70.23742500.9460.1430.2771.00698.5
1.55-1.653.70.16942140.9710.1020.1971.02198.8
1.65-1.783.70.12342610.9830.0750.1441.02699
1.78-1.963.70.07842740.9930.0470.0911.01699.1
1.96-2.243.60.05642990.9950.0350.0661.00699.4
2.24-2.823.60.03743130.9980.0230.0441.03599.5
2.82-303.50.03343020.9980.0210.0391.02697.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRM

1wrm


Resolution: 1.31→22.53 Å / SU ML: 0.1576 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 2000 4.71 %
Rwork0.1874 40475 -
obs0.1879 42475 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.79 Å2
Refinement stepCycle: final / Resolution: 1.31→22.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 5 154 1400
Biso mean--13.37 29.15 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461273
X-RAY DIFFRACTIONf_angle_d0.79211718
X-RAY DIFFRACTIONf_chiral_restr0.0684184
X-RAY DIFFRACTIONf_plane_restr0.0044222
X-RAY DIFFRACTIONf_dihedral_angle_d12.2657473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.340.32611390.26932814X-RAY DIFFRACTION96.35
1.34-1.380.26121410.26082836X-RAY DIFFRACTION97.7
1.38-1.420.26151410.23242877X-RAY DIFFRACTION97.92
1.42-1.460.24641410.21232846X-RAY DIFFRACTION98.06
1.46-1.520.23611420.20382881X-RAY DIFFRACTION98.34
1.52-1.580.20691420.19372876X-RAY DIFFRACTION98.21
1.58-1.650.19641440.18792887X-RAY DIFFRACTION99.12
1.65-1.740.22441430.18342911X-RAY DIFFRACTION98.87
1.74-1.840.21151440.18222915X-RAY DIFFRACTION99.29
1.84-1.990.17481430.18092900X-RAY DIFFRACTION99.25
1.99-2.190.18351450.1762922X-RAY DIFFRACTION99.32
2.19-2.50.18971450.18942933X-RAY DIFFRACTION99.42
2.5-3.150.22511450.18872943X-RAY DIFFRACTION99.68
3.15-22.530.15881450.17332934X-RAY DIFFRACTION97.22

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