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- PDB-6l1s: Crystal structure of DUSP22 mutant_C88S -

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Basic information

Entry
Database: PDB / ID: 6l1s
TitleCrystal structure of DUSP22 mutant_C88S
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
PHOSPHATE ION / Dual specificity protein phosphatase 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3611 Å
AuthorsLai, C.H. / Chang, C.C. / Lyu, P.C.
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
DepositionSep 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low

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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)17,8902
Polymers17,7951
Non-polymers951
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.615, 49.714, 39.823
Angle α, β, γ (deg.)90.000, 94.720, 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: 17795.314 Da / Num. of mol.: 1 / Mutation: C88S
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.: 185 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.2M Imidazole, 0.4M NaH2PO4/1.6M K2HPO4, 0.2M NaCl

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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 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→30 Å / Num. obs: 36409 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.02 / Rrim(I) all: 0.039 / Χ2: 1.046 / Net I/σ(I): 20.6 / Num. measured all: 137519
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.36-1.413.80.22735500.9610.1340.2641.05595.9
1.41-1.473.80.16136090.9820.0950.1871.01696.1
1.47-1.533.80.12535710.9880.0740.1451.01396.7
1.53-1.613.80.0936080.9930.0540.1051.01197.1
1.61-1.713.80.07636550.9950.0450.0881.07697.3
1.71-1.853.80.06236350.9950.0370.0721.04697.9
1.85-2.033.80.04336950.9980.0250.050.99698.5
2.03-2.333.80.03737000.9970.0220.0431.10398.8
2.33-2.933.80.03137250.9980.0180.0360.95299.2
2.93-303.60.02336610.9990.0140.0271.19895.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.98 Å22.33 Å
Translation4.98 Å22.33 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX2.8.3phasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRM

1wrm


Resolution: 1.3611→22.3308 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.1954 1968 5.41 %
Rwork0.1797 --
obs0.1805 36406 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 44.17 Å2 / Biso mean: 19.1077 Å2 / Biso min: 8.98 Å2
Refinement stepCycle: final / Resolution: 1.3611→22.3308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 5 185 1438
Biso mean--11.84 29.74 -
Num. residues----157
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3611-1.39510.20241480.213233194
1.3951-1.43280.2261330.2023244096
1.4328-1.4750.21111420.197243496
1.475-1.52260.22641400.193243397
1.5226-1.5770.20721240.188243397
1.577-1.64010.21961480.1857246697
1.6401-1.71470.21241390.1865245897
1.7147-1.80510.20631270.1822248398
1.8051-1.91810.19291550.1828246398
1.9181-2.06610.18981450.1821247898
2.0661-2.27390.1881430.1756251099
2.2739-2.60250.18881550.1893251299
2.6025-3.27720.21781360.1776255099
3.2772-22.33080.17171330.165244794

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