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- PDB-6lmy: Crystal structure of DUSP22 mutant_C88S/S93A -

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Basic information

Entry
Database: PDB / ID: 6lmy
TitleCrystal structure of DUSP22 mutant_C88S/S93A
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: 1.5 Å
AuthorsLai, C.H. / 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
DepositionDec 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8742
Polymers17,7791
Non-polymers951
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.680, 50.147, 39.699
Angle α, β, γ (deg.)90.000, 94.900, 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: 17779.314 Da / Num. of mol.: 1 / Mutation: C88S,S93A
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.: 111 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M imidazole, 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: 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: 1.5→30 Å / Num. obs: 28189 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Χ2: 1.015 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.553.40.62528020.7420.3930.7411.0299.7
1.55-1.623.60.51827930.8380.3150.6071.01199.8
1.62-1.693.70.40728350.9010.2450.4761.01499.8
1.69-1.783.70.28828280.9350.1730.3361.01899.9
1.78-1.893.70.20227940.9690.1230.2371.00499.8
1.89-2.043.70.11828110.9880.0720.1381.01899.8
2.04-2.243.60.0828410.9920.0490.0941.00199.8
2.24-2.563.60.06328330.9950.0390.0741.01499.9
2.56-3.233.70.03828350.9980.0230.0451.01999.7
3.23-303.40.02228170.9990.0140.0261.02896.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5 Å25.61 Å
Translation5 Å25.61 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: 1.5→25.61 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.84
RfactorNum. reflection% reflection
Rfree0.2129 2014 7.15 %
Rwork0.182 --
obs0.1842 28187 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.21 Å2 / Biso mean: 22.5903 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 1.5→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 5 111 1359
Biso mean--15.57 32.49 -
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 (%)
1.5-1.530.26751400.2592179596
1.53-1.580.27121480.22741866100
1.58-1.620.24181400.22311851100
1.62-1.670.24951570.211855100
1.67-1.730.23351480.20141888100
1.73-1.80.21151410.19561865100
1.8-1.890.22151470.19011879100
1.89-1.990.19871550.19081881100
1.99-2.110.19961360.17871851100
2.11-2.270.18691400.18451889100
2.27-2.50.2171450.19071903100
2.5-2.860.22561350.19021882100
2.86-3.60.22761470.1751897100
3.6-25.610.18691350.1515187196

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