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- PDB-6lot: Crystal structure of DUSP22 mutant_N128D -

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Basic information

Entry
Database: PDB / ID: 6lot
TitleCrystal structure of DUSP22 mutant_N128D
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 non-membrane spanning protein tyrosine kinase activity / negative regulation of T cell mediated immunity / leading edge of lamellipodium / negative regulation of T cell activation / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / myosin phosphatase activity / protein-serine/threonine phosphatase / filamentous actin ...negative regulation of non-membrane spanning protein tyrosine kinase activity / negative regulation of T cell mediated immunity / leading edge of lamellipodium / negative regulation of T cell activation / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / myosin phosphatase activity / protein-serine/threonine phosphatase / filamentous actin / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / dephosphorylation / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of JNK cascade / regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / 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: 1.69 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
DepositionJan 7, 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)17,9082
Polymers17,8121
Non-polymers961
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-18 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.278, 50.686, 41.097
Angle α, β, γ (deg.)90.000, 91.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

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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: 17812.367 Da / Num. of mol.: 1 / Mutation: N128D
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.1 M PIPES, 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: TPS 05A / Wavelength: 0.99984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. obs: 20649 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Χ2: 1.007 / Net I/σ(I): 16.6 / Num. measured all: 72939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.69-1.753.30.3519260.8990.2220.4160.99492.4
1.75-1.823.50.2720680.9440.1670.3191.00198.9
1.82-1.93.60.19120660.9740.1160.2241.01399.5
1.9-23.70.13520770.9850.0820.1580.99999.6
2-2.133.70.09720830.990.0590.1141.00399.1
2.13-2.293.70.07120680.9930.0440.0831.0299.4
2.29-2.523.60.05720910.9960.0350.0670.99799.6
2.52-2.893.50.05320850.9950.0330.0631.02199.4
2.89-3.643.40.03720860.9980.0230.0441.01398.6
3.64-303.40.02120990.9990.0130.0251.00597.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.07 Å25.87 Å
Translation5.07 Å25.87 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRM

1wrm


Resolution: 1.69→25.8736 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.65
RfactorNum. reflection% reflection
Rfree0.2192 1987 9.65 %
Rwork0.1919 --
obs0.1946 20584 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.22 Å2 / Biso mean: 25.5385 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 1.69→25.8736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 5 78 1294
Biso mean--19.42 33.57 -
Num. residues----151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.69-1.73230.30581380.2391122792
1.7323-1.77910.26121360.2302130898
1.7791-1.83150.19531370.2157131599
1.8315-1.89060.25851390.1956135699
1.8906-1.95810.22811480.1973134199
1.9581-2.03650.21411440.2031133399
2.0365-2.12910.22731390.1887132499
2.1291-2.24130.21671380.1916134199
2.2413-2.38160.23791330.20251358100
2.3816-2.56540.23331420.2181133799
2.5654-2.82330.21871490.20151335100
2.8233-3.23110.23681450.1975134699
3.2311-4.06830.22521420.1733133598
4.0683-25.87360.17951570.1698134197

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