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- PDB-4jmk: Structure of dusp8 -

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Basic information

Entry
Database: PDB / ID: 4jmk
TitleStructure of dusp8
ComponentsDual specificity protein phosphatase 8
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / 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 S7 phosphatase activity ...protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / 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 S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / dephosphorylation / protein-serine/threonine phosphatase / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / Negative regulation of MAPK pathway / signal transduction / nucleus / cytoplasm
Similarity search - Function
: / Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. ...: / Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJeong, D.G. / Kim, S.J. / Ryu, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The family-wide structure and function of human dual-specificity protein phosphatases.
Authors: Jeong, D.G. / Wei, C.H. / Ku, B. / Jeon, T.J. / Chien, P.N. / Kim, J.K. / Park, S.Y. / Hwang, H.S. / Ryu, S.Y. / Park, H. / Kim, D.S. / Kim, S.J. / Ryu, S.E.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 8
B: Dual specificity protein phosphatase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7006
Polymers34,3162
Non-polymers3844
Water2,828157
1
A: Dual specificity protein phosphatase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3503
Polymers17,1581
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3503
Polymers17,1581
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.850, 65.850, 124.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Dual specificity protein phosphatase 8 / Dual specificity protein phosphatase hVH-5


Mass: 17157.938 Da / Num. of mol.: 2 / Fragment: UNP residues 160-310 / Mutation: C246S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP8, C11orf81, VH5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13202, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Hepes, PEG 8000, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2006
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 22431 / Num. obs: 22371 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZZW

1zzw


Resolution: 1.9→35.109 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.19 / σ(F): 0 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1084 4.86 %
Rwork0.1763 21223 -
obs0.1777 22307 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.37 Å2 / Biso mean: 27.802 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 20 157 2522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082406
X-RAY DIFFRACTIONf_angle_d1.1193249
X-RAY DIFFRACTIONf_dihedral_angle_d14.219914
X-RAY DIFFRACTIONf_chiral_restr0.079364
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.98650.2531260.193125962722
1.9865-2.09120.28331500.18425612711
2.0912-2.22220.22471440.177526142758
2.2222-2.39380.24551350.186626102745
2.3938-2.63460.2331490.177326322781
2.6346-3.01560.17761170.178626622779
3.0156-3.79860.18991350.167526862821
3.7986-35.11530.17911280.174128622990
Refinement TLS params.Method: refined / Origin x: 14.8396 Å / Origin y: -4.8995 Å / Origin z: 4.4359 Å
111213212223313233
T0.1279 Å2-0.009 Å2-0.0118 Å2-0.1188 Å2-0.003 Å2--0.1211 Å2
L1.3078 °2-0.1884 °2-0.5351 °2-0.2934 °20.093 °2--0.5517 °2
S0.0056 Å °-0.1745 Å °0.1242 Å °-0.0239 Å °0.0468 Å °-0.0192 Å °-0.0362 Å °0.0425 Å °0.004 Å °
Refinement TLS groupSelection details: all

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