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- PDB-5gtj: CRYSTAL STRUCTURE OF CATALYTICALLY ACTIVE FORM OF HUMAN DUSP26 -

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Basic information

Entry
Database: PDB / ID: 5gtj
TitleCRYSTAL STRUCTURE OF CATALYTICALLY ACTIVE FORM OF HUMAN DUSP26
ComponentsDual specificity protein phosphatase 26
KeywordsHYDROLASE / Active form
Function / homology
Function and homology information


MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / p53 binding / RNA polymerase II-specific DNA-binding transcription factor binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Atypical dual specificity phosphatase, subfamily A / 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 ...Atypical dual specificity phosphatase, subfamily A / 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
PHOSPHATE ION / Dual specificity protein phosphatase 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWon, E.-Y. / Kim, S.J. / Chi, S.-W.
CitationJournal: Plos One / Year: 2016
Title: Structural Insight into the Critical Role of the N-Terminal Region in the Catalytic Activity of Dual-Specificity Phosphatase 26
Authors: Won, E.Y. / Lee, S.O. / Lee, D.H. / Lee, D. / Bae, K.H. / Lee, S.C. / Kim, S.J. / Chi, S.W.
History
DepositionAug 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 26
B: Dual specificity protein phosphatase 26
C: Dual specificity protein phosphatase 26
D: Dual specificity protein phosphatase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1238
Polymers82,7434
Non-polymers3804
Water8,593477
1
A: Dual specificity protein phosphatase 26
B: Dual specificity protein phosphatase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5614
Polymers41,3712
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-43 kcal/mol
Surface area15710 Å2
MethodPISA
2
C: Dual specificity protein phosphatase 26
D: Dual specificity protein phosphatase 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5614
Polymers41,3712
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-45 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.617, 100.803, 70.870
Angle α, β, γ (deg.)90.00, 114.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Dual specificity protein phosphatase 26 / Dual specificity phosphatase SKRP3 / Low-molecular-mass dual-specificity phosphatase 4 / LDP-4 / ...Dual specificity phosphatase SKRP3 / Low-molecular-mass dual-specificity phosphatase 4 / LDP-4 / Mitogen-activated protein kinase phosphatase 8 / MKP-8 / Novel amplified gene in thyroid anaplastic cancer


Mass: 20685.674 Da / Num. of mol.: 4 / Mutation: C152S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP26, DUSP24, LDP4, MKP8, NATA1, SKRP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: Q9BV47, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 291 K / Method: microbatch / Details: 0.1M Tris-HCl pH 8.5, 0.9M potassium thiocyanate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→39.691 Å / Num. obs: 53434 / % possible obs: 97.2 % / Redundancy: 4.9 % / Net I/σ(I): 17.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.691 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 25.36
RfactorNum. reflection% reflection
Rfree0.2527 2645 5.1 %
Rwork0.1958 --
obs0.1987 51819 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 20 477 5849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075493
X-RAY DIFFRACTIONf_angle_d0.917431
X-RAY DIFFRACTIONf_dihedral_angle_d19.9023248
X-RAY DIFFRACTIONf_chiral_restr0.05811
X-RAY DIFFRACTIONf_plane_restr0.005954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03640.35691210.2912534X-RAY DIFFRACTION94
2.0364-2.07550.31941320.28912496X-RAY DIFFRACTION96
2.0755-2.11790.32031370.27112493X-RAY DIFFRACTION95
2.1179-2.16390.35311340.26442544X-RAY DIFFRACTION97
2.1639-2.21430.29361600.23452540X-RAY DIFFRACTION97
2.2143-2.26960.25841400.22392578X-RAY DIFFRACTION97
2.2696-2.3310.25821470.2172537X-RAY DIFFRACTION97
2.331-2.39960.28841320.21682567X-RAY DIFFRACTION97
2.3996-2.4770.26141520.20352571X-RAY DIFFRACTION98
2.477-2.56550.30761490.20612576X-RAY DIFFRACTION98
2.5655-2.66820.27461320.20022595X-RAY DIFFRACTION98
2.6682-2.78960.2781390.21092585X-RAY DIFFRACTION99
2.7896-2.93670.28081350.2082654X-RAY DIFFRACTION99
2.9367-3.12060.29931460.20442586X-RAY DIFFRACTION99
3.1206-3.36140.26651370.19512654X-RAY DIFFRACTION100
3.3614-3.69950.22651390.17792633X-RAY DIFFRACTION100
3.6995-4.23430.20621420.15362664X-RAY DIFFRACTION100
4.2343-5.33270.19571270.1552670X-RAY DIFFRACTION100
5.3327-39.69850.20721440.18552697X-RAY DIFFRACTION100

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