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- PDB-4jnb: Crystal structure of the Catalytic Domain of Human DUSP12 -

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Basic information

Entry
Database: PDB / ID: 4jnb
TitleCrystal structure of the Catalytic Domain of Human DUSP12
ComponentsDual specificity protein phosphatase 12
KeywordsHYDROLASE / DUSP / Dual specificity phosphatase / phosphatase
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein modification process / kinase binding / zinc ion binding ...protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein modification process / kinase binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity protein phosphatase 12 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Zinc finger C2H2 type domain profile. / Tyrosine-specific protein phosphatases domain ...Dual specificity protein phosphatase 12 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Zinc finger C2H2 type domain profile. / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Zinc finger C2H2-type / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJeon, T.J. / Chien, P.N. / Ku, B. / 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 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7152
Polymers18,6191
Non-polymers961
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.380, 127.380, 40.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Dual specificity protein phosphatase 12 / Dual specificity tyrosine phosphatase YVH1


Mass: 18619.234 Da / Num. of mol.: 1 / Fragment: catalytic domain UNP RESIDUES 27-193 / Mutation: C97A, C115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP12 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UNI6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris pH 8.5, 1.9M Ammonium sulfate, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 4743

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å
RfactorNum. reflection
Rfree0.253 -
Rwork0.247 -
all-4878
obs-4743
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 5 0 1257

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