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- PDB-2esb: Crystal structure of human DUSP18 -

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Basic information

Entry
Database: PDB / ID: 2esb
TitleCrystal structure of human DUSP18
ComponentsDual specificity protein phosphatase 18
KeywordsHYDROLASE / alpha/beta structure
Function / homology
Function and homology information


protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / MAP kinase tyrosine/serine/threonine phosphatase activity / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / peptidyl-tyrosine dephosphorylation / dephosphorylation / protein-tyrosine-phosphatase ...protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / MAP kinase tyrosine/serine/threonine phosphatase activity / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / peptidyl-tyrosine dephosphorylation / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitochondrial inner membrane / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Atypical dual specificity phosphatase, subfamily B / 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 / Tyrosine specific protein phosphatases active site. ...: / Atypical dual specificity phosphatase, subfamily B / 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 / 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
ACETATE ION / Dual specificity protein phosphatase 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, S.J. / Ryu, S.E. / Jeong, D.G. / Cho, Y.H. / Yoon, T.S. / Kim, J.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of human DSP18, a member of the dual-specificity protein tyrosine phosphatase family.
Authors: Jeong, D.G. / Cho, Y.H. / Yoon, T.S. / Kim, J.H. / Son, J.H. / Ryu, S.E. / Kim, S.J.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3853
Polymers21,0871
Non-polymers2972
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.740, 96.083, 116.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1160-

HOH

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Components

#1: Protein Dual specificity protein phosphatase 18 / Dual Specific Phosphatase 18 / Low molecular weight dual specificity phosphatase 20


Mass: 21087.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NEJ0, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH, 10% isopropanol, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 13478 / Num. obs: 13478 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.107 / Rsym value: 0.107
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.196 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS0.9refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.189 685 random
Rwork0.159 --
all0.161 13478 -
obs0.161 13478 -
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 19 169 1457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.7

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