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- PDB-2g6z: Crystal structure of human DUSP5 -

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Basic information

Entry
Database: PDB / ID: 2g6z
TitleCrystal structure of human DUSP5
ComponentsDual specificity protein phosphatase 5
KeywordsHYDROLASE / alpha/beta
Function / homology
Function and homology information


: / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / : / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / RAF-independent MAPK1/3 activation ...: / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / : / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / RAF-independent MAPK1/3 activation / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Negative regulation of MAPK pathway / MAPK cascade / nucleoplasm / 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 / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...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 / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKim, S.J. / Ryu, S.E.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of the catalytic domain of human DUSP5, a dual specificity MAP kinase protein phosphatase
Authors: Jeong, D.G. / Cho, Y.H. / Yoon, T.S. / Kim, J.H. / Ryu, S.E. / Kim, S.J.
History
DepositionFeb 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 5
B: Dual specificity protein phosphatase 5
C: Dual specificity protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0559
Polymers69,4783
Non-polymers5766
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.712, 92.712, 165.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-34-

HOH

DetailsThe biological assembly is dimer

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Components

#1: Protein Dual specificity protein phosphatase 5 / DUSP5 / Dual specificity protein phosphatase hVH3 / Tyrosine-protein phosphatase


Mass: 23159.467 Da / Num. of mol.: 3 / Fragment: residues 174-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q16690, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 2.2M ammonium sulfate and 6% (v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2004
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 20822 / Num. obs: 20524 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.291 980 random
Rwork0.244 --
all0.248 20822 -
obs0.248 20524 -
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 30 39 3548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.37
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.99

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