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- PDB-3s4e: Crystal Structrue of a Novel Mitogen-activated Protein Kinase Pho... -

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Basic information

Entry
Database: PDB / ID: 3s4e
TitleCrystal Structrue of a Novel Mitogen-activated Protein Kinase Phosphatase, SKRP1
ComponentsDual specificity protein phosphatase 19
KeywordsHYDROLASE / PTP / protein tyrosine phosphatase / phosphatase
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 / myosin phosphatase activity / protein-serine/threonine phosphatase / protein kinase activator activity / protein kinase inhibitor 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 / myosin phosphatase activity / protein-serine/threonine phosphatase / protein kinase activator activity / protein kinase inhibitor activity / positive regulation of protein kinase activity / positive regulation of JUN kinase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of JNK cascade / negative regulation of protein kinase activity / 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
PHOSPHATE ION / Dual specificity protein phosphatase 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsWei, C.H. / Ryu, S.Y. / Jeon, Y.H. / Jeong, D.G. / Kim, S.J. / Ryu, S.E.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of a novel mitogen-activated protein kinase phosphatase, SKRP1.
Authors: Wei, C.H. / Ryu, S.Y. / Jeon, Y.H. / Yoon, M.Y. / Jeong, D.G. / Kim, S.J. / Ryu, S.E.
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)16,1804
Polymers15,8931
Non-polymers2873
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.852, 50.313, 57.872
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 SKRP1 / Stress-activated protein kinase pathway-regulating phosphatase 1 / SAPK pathway-regulating phosphatase 1


Mass: 15893.014 Da / Num. of mol.: 1 / Fragment: PTP-loop (UNP RESIDUES 65-206) / Mutation: C150S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP19, DUSP17, LMWDSP3, SKRP1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q8WTR2, 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2.0M ammonium sulfate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. all: 487871 / Num. obs: 487871 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 64.081
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.091 / Mean I/σ(I) obs: 31.945 / Num. unique all: 487871 / Rsym value: 0.091 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZZW

1zzw


Resolution: 1.26→37.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.101 / SU ML: 0.023 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 1778 4.9 %RANDOM
Rwork0.1505 ---
all0.1509 37655 --
obs0.152 34279 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.26→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 15 210 1343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9691561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8522550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87715196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.242154
X-RAY DIFFRACTIONr_chiral_restr0.110.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021851
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9951.5716
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.76821155
X-RAY DIFFRACTIONr_scbond_it3.983436
X-RAY DIFFRACTIONr_scangle_it5.3484.5406
X-RAY DIFFRACTIONr_rigid_bond_restr2.27131152
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 141 -
Rwork0.148 2582 -
obs--99.96 %

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