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- PDB-4d3r: Crystal structure of point mutated DUSP19 (I187A) -

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Basic information

Entry
Database: PDB / ID: 4d3r
TitleCrystal structure of point mutated DUSP19 (I187A)
ComponentsDUAL SPECIFICITY PROTEIN PHOSPHATASE 19
KeywordsHYDROLASE
Function / homology
Function and homology information


JUN kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / negative regulation of JNK cascade / mitogen-activated protein kinase kinase kinase binding / regulation of JNK cascade / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity ...JUN kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / negative regulation of JNK cascade / mitogen-activated protein kinase kinase kinase binding / regulation of JNK cascade / histone H2AXS140 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 / protein kinase inhibitor activity / protein kinase activator activity / positive regulation of protein kinase activity / positive regulation of JUN kinase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of protein kinase activity / positive regulation of JNK cascade / positive regulation of MAPK cascade / 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
Dual specificity protein phosphatase 19
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsJeon, T.J. / Nam, K.T. / Ryu, S.E.
CitationJournal: Biodesign / Year: 2015
Title: Structural Analysis of Activity-Modulating Mutations of Dusp19
Authors: Jeon, T.J. / Nam, K.T. / Ryu, S.E.
History
DepositionOct 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5732
Polymers15,4771
Non-polymers961
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.396, 47.934, 57.477
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 19 / DUAL SPECIFICITY PHOSPHATASE TS-DSP1 / LOW MOLECULAR WEIGHT DUAL SPECIFICITY PHOSPHATASE 3 / LMW- ...DUAL SPECIFICITY PHOSPHATASE TS-DSP1 / LOW MOLECULAR WEIGHT DUAL SPECIFICITY PHOSPHATASE 3 / LMW-DSP3 / PROTEIN PHOSPHATASE SKRP 1 / STRESS-ACTIVATED PROTEIN KINASE PATHWAY-REGULATING PHOSPHATASE 1 / SAPK PATHWAY-REGULATING PHOSPHATASE 1


Mass: 15476.587 Da / Num. of mol.: 1 / Fragment: PHOSPHATASE DOMAINS, RESIDUES 65-204 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: Q8WTR2, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.18 Å3/Da / Density % sol: 43.52 % / Description: NONE
Crystal growDetails: 1.9M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 16565 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 32.2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S4E

3s4e


Resolution: 1.67→6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.425 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19905 754 5 %RANDOM
Rwork0.16091 ---
obs0.16272 14357 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.567 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.67→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 5 115 1209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191115
X-RAY DIFFRACTIONr_bond_other_d0.0010.021064
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.9591510
X-RAY DIFFRACTIONr_angle_other_deg0.95532450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36424.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29515190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.258154
X-RAY DIFFRACTIONr_chiral_restr0.1430.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 67 -
Rwork0.151 985 -
obs--100 %

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