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- PDB-8tk3: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidi... -

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Basic information

Entry
Database: PDB / ID: 8tk3
TitleHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidized catalytic cysteine and complexed with 6-(difluoromethyl)pyrimidin-4-ol at two allosteric sites
ComponentsDual specificity protein phosphatase 3
KeywordsHYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE / VHR
Function / homology
Function and homology information


receptor signaling protein tyrosine kinase inhibitor activity / MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / ERKs are inactivated / dephosphorylation / negative regulation of JNK cascade / motile cilium ...receptor signaling protein tyrosine kinase inhibitor activity / MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / ERKs are inactivated / dephosphorylation / negative regulation of JNK cascade / motile cilium / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / protein serine/threonine phosphatase activity / phosphatase activity / peptidyl-tyrosine dephosphorylation / immunological synapse / negative regulation of MAPK cascade / cytoskeletal protein binding / protein-tyrosine-phosphatase / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cytoskeleton / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Atypical dual specificity phosphatase, subfamily A / 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 active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
: / Dual specificity protein phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAleshin, A.E. / Wu, J. / Lambert, L.J. / Cosford, N.D.P. / Tautz, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21 AI160161 United States
CitationJournal: Acs Omega / Year: 2025
Title: Fragment Screening Identifies Novel Allosteric Binders and Binding Sites in the VHR ( DUSP3 ) Phosphatase.
Authors: Wu, J. / Baranowski, M.R. / Aleshin, A.E. / Isiorho, E.A. / Lambert, L.J. / De Backer, L.J.S. / Han, Y.N. / Das, R. / Sheffler, D.J. / Bobkov, A.A. / Lemberikman, A.M. / Keedy, D.A. / Cosford, N.D.P. / Tautz, L.
History
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 26, 2025Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / reflns / reflns_shell
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_redundancy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8426
Polymers20,3151
Non-polymers5275
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.133, 52.467, 100.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity protein phosphatase 3 / Dual specificity protein phosphatase VHR / Vaccinia H1-related phosphatase / VHR


Mass: 20315.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cys123 is oxidized to sulfinic acid / Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP3, VHR / Production host: Escherichia coli (E. coli)
References: UniProt: P51452, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-I2X / 6-(difluoromethyl)pyrimidin-4-ol / ISOTHIAZOLIDANONE ANALOGUE


Mass: 146.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4F2N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: The protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the crystallization buffer (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the ...Details: The protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the crystallization buffer (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the crystallization buffer. The crystals were soaked with 25 mM of the compound in solution (10% DMSO, 100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.95→50.3 Å / Num. obs: 13585 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8
Reflection shellResolution: 1.95→2.18 Å / Redundancy: 7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3842 / CC1/2: 0.91 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.093 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25538 632 5 %RANDOM
Rwork0.18617 ---
obs0.18968 12090 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.256 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2--4.85 Å2-0 Å2
3----2.02 Å2
Refinement stepCycle: 1 / Resolution: 2→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 32 106 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161433
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6472031
X-RAY DIFFRACTIONr_angle_other_deg0.5181.5753288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.46512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84610261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021822
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
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_it2.7683.046745
X-RAY DIFFRACTIONr_mcbond_other2.7683.045745
X-RAY DIFFRACTIONr_mcangle_it4.1385.461940
X-RAY DIFFRACTIONr_mcangle_other4.1415.465941
X-RAY DIFFRACTIONr_scbond_it3.8993.544755
X-RAY DIFFRACTIONr_scbond_other3.8963.55756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9086.3051092
X-RAY DIFFRACTIONr_long_range_B_refined8.29935.151753
X-RAY DIFFRACTIONr_long_range_B_other8.27134.551734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 45 -
Rwork0.312 860 -
obs--100 %

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