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- PDB-6lvq: Crystal structure of DUSP22_VO4 -

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Basic information

Entry
Database: PDB / ID: 6lvq
TitleCrystal structure of DUSP22_VO4
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
VANADATE ION / Dual specificity protein phosphatase 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 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
DepositionFeb 4, 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)17,9262
Polymers17,8111
Non-polymers1151
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-3 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.130, 49.736, 39.847
Angle α, β, γ (deg.)90.000, 108.130, 90.000
Int Tables number4
Space group name H-MP1211

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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: 17811.381 Da / Num. of mol.: 1
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-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, 2 mM MnCl2, 0.1 mM VO4, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 27144 / % possible obs: 97.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.048 / Rrim(I) all: 0.118 / Χ2: 1.062 / Net I/σ(I): 9.8 / Num. measured all: 152760
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.38-1.433.30.57826220.8060.3530.681.08795.1
1.43-1.493.70.61326720.7460.3390.7031.09497.1
1.49-1.554.50.69126710.880.3290.7671.07697.3
1.55-1.6460.80227310.8990.3390.8721.07598
1.64-1.746.90.61426980.9550.2470.6631.08798.2
1.74-1.8770.35627260.980.1430.3841.06898.5
1.87-2.066.80.1827410.9920.0740.1951.05299
2.06-2.366.60.10427630.9940.0430.1131.04499
2.36-2.976.60.07327570.9960.0310.0791.04999.5
2.97-504.70.04427630.9950.0240.0511.00596.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.38 Å28.26 Å
Translation1.38 Å28.26 Å

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Processing

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

1wrm


Resolution: 1.38→28.2624 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.2287 2000 7.39 %
Rwork0.2041 --
obs0.206 27061 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 45.74 Å2 / Biso mean: 20.2221 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: final / Resolution: 1.38→28.2624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 5 98 1351
Biso mean--16.48 28.37 -
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 (%)
1.38-1.41450.29221350.2772168993
1.4145-1.45280.2611390.2491175597
1.4528-1.49550.29971430.2483177597
1.4955-1.54380.29891400.2349176497
1.5438-1.59890.22871440.2235179798
1.5989-1.6630.25291420.2302178198
1.663-1.73860.26521420.2201178599
1.7386-1.83030.25451440.2068179698
1.8303-1.94490.2021440.2067181399
1.9449-2.09510.26121450.2081181199
2.0951-2.30580.22341440.1986181499
2.3058-2.63920.22871480.20291846100
2.6392-3.32430.2141460.1953183699
3.3243-28.26240.20451440.1864179996

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