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- PDB-6lou: Crystal structure of DUSP22 mutant_C88S/S93N -

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Basic information

Entry
Database: PDB / ID: 6lou
TitleCrystal structure of DUSP22 mutant_C88S/S93N
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 / negative regulation of cell migration / cellular response to epidermal growth factor stimulus / positive regulation of JNK cascade / regulation of cell population proliferation / intracellular signal transduction / negative regulation of transcription by RNA polymerase II / 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 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
PHOSPHATE ION / Dual specificity protein phosphatase 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5301 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)17,9172
Polymers17,8221
Non-polymers951
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.049, 50.226, 40.938
Angle α, β, γ (deg.)90.000, 93.550, 90.000
Int Tables number5
Space group name H-MC121

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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: 17822.340 Da / Num. of mol.: 1 / Mutation: C88S,S93N
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M arginine, 0.05 M glutamic acid, 0.4 M NaH2PO4, 1.6 M K2HPO4, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. obs: 27127 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Χ2: 1.015 / Net I/σ(I): 26.8 / Num. measured all: 92975
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.582.50.24724790.9230.1870.3121.02591
1.58-1.652.80.21326530.9520.1510.2631.01396.4
1.65-1.723.30.17827110.9710.1130.2121.03998.6
1.72-1.813.70.13727100.9850.0830.1611.02199.3
1.81-1.933.70.08927510.9930.0540.1041.01799.5
1.93-2.083.60.06227380.9960.0380.0730.99999.7
2.08-2.293.60.04727470.9970.0290.0551.01299.5
2.29-2.623.70.03627500.9980.0220.0431.01100
2.62-3.293.70.02527780.9990.0150.031.0299.7
3.29-303.50.02228100.9990.0130.0250.99799.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.08 Å22.47 Å
Translation5.08 Å22.47 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: 1.5301→22.4714 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.22
RfactorNum. reflection% reflection
Rfree0.1957 2014 7.43 %
Rwork0.1717 --
obs0.1735 27122 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.46 Å2 / Biso mean: 19.7138 Å2 / Biso min: 8.25 Å2
Refinement stepCycle: final / Resolution: 1.5301→22.4714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 5 133 1384
Biso mean--11.96 29.61 -
Num. residues----156
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5301-1.56830.21981390.2107160989
1.5683-1.61070.19311260.2027172395
1.6107-1.65810.21321560.1914174397
1.6581-1.71160.21231390.1767180899
1.7116-1.77270.18851350.1728179199
1.7727-1.84370.20511550.1749181599
1.8437-1.92760.18481390.1705180199
1.9276-2.02910.16751500.172180499
2.0291-2.15620.19621530.16491823100
2.1562-2.32250.21441440.1755180699
2.3225-2.55590.22511440.18411846100
2.5559-2.92510.20521480.17841831100
2.9251-3.68260.20181370.1641840100
3.6826-22.47140.16741490.1572186899

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