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- PDB-4woh: Structure of of human dual-specificity phosphatase 22 (E24A/K28A/... -

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Basic information

Entry
Database: PDB / ID: 4woh
TitleStructure of of human dual-specificity phosphatase 22 (E24A/K28A/K30A/C88S) complexed with 4-nitrophenolphosphate
ComponentsDual specificity protein phosphatase 22
KeywordsHYDROLASE / dual specificity phosphatase / JSP-1 / pNPP
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 / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 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 / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / filamentous actin / immune system process / protein tyrosine phosphatase activity / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / protein-tyrosine-phosphatase / non-membrane spanning protein tyrosine phosphatase activity / transforming growth factor beta receptor signaling pathway / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / protein tyrosine kinase binding / 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 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like ...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 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
4-NITROPHENYL PHOSPHATE / DI(HYDROXYETHYL)ETHER / Dual specificity protein phosphatase 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsLountos, G.T. / Cherry, S. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate.
Authors: Lountos, G.T. / Cherry, S. / Tropea, J.E. / Waugh, D.S.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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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)18,9354
Polymers18,5481
Non-polymers3873
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.816, 49.632, 39.899
Angle α, β, γ (deg.)90.00, 94.88, 90.00
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: 18548.002 Da / Num. of mol.: 1 / Mutation: E24A/K28A/K30A/C88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP22, JSP1, LMWDSP2, MKPX / Plasmid: pJT294 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRW4, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-4NP / 4-NITROPHENYL PHOSPHATE


Mass: 219.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6NO6P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21 mg/mL protein incubated with 10 mM 4-ntirophenolphosphate well solution: 0.1M Tris pH 8.5, 0.2M magnesium chloride, 20% w/v polyethylene glycol 3350
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 37336 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rsym value: 0.035 / Net I/σ(I): 48.2
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8

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Processing

SoftwareName: REFMAC / Version: 5.5.0104 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1wrm

1wrm


Resolution: 1.34→44.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.363 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16499 1864 5 %RANDOM
Rwork0.14028 ---
obs0.14151 35466 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.159 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.56 Å2
2--0.13 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.34→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 25 193 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211393
X-RAY DIFFRACTIONr_bond_other_d0.0010.02952
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9621904
X-RAY DIFFRACTIONr_angle_other_deg0.86532327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40223.33363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13115234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7871510
X-RAY DIFFRACTIONr_chiral_restr0.070.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1431.5848
X-RAY DIFFRACTIONr_mcbond_other0.3341.5344
X-RAY DIFFRACTIONr_mcangle_it1.89621376
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6483545
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1394.5518
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.95332345
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.342→1.377 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 122 -
Rwork0.294 2145 -
obs--78.88 %

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