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- PDB-9y55: A crystal structure of DUSP10 loop mutant I445A -

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Basic information

Entry
Database: PDB / ID: 9y55
TitleA crystal structure of DUSP10 loop mutant I445A
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE / MAP kinase phosphatase / Mutant
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / negative regulation of oligodendrocyte differentiation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / negative regulation of oligodendrocyte differentiation / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / dephosphorylation / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / positive regulation of regulatory T cell differentiation / mitogen-activated protein kinase p38 binding / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / oligodendrocyte differentiation / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / protein-tyrosine-phosphatase / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / negative regulation of epithelial cell proliferation / Negative regulation of MAPK pathway / response to lipopolysaccharide / signal transduction / nucleoplasm / nucleus / cytoplasm / cytosol
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. / 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 profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.502 Å
AuthorsManjula, R. / Lolis, E.J. / Bennett, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Functional coupling of alpha4 alpha5 loop to allosteric site on MKP5 as a critical determinant of catalysis.
Authors: Manjula, R. / Lolis, E.J.
History
DepositionSep 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10
C: Dual specificity protein phosphatase 10
D: Dual specificity protein phosphatase 10
E: Dual specificity protein phosphatase 10
F: Dual specificity protein phosphatase 10
G: Dual specificity protein phosphatase 10
H: Dual specificity protein phosphatase 10
I: Dual specificity protein phosphatase 10
J: Dual specificity protein phosphatase 10
K: Dual specificity protein phosphatase 10
L: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)204,29412
Polymers204,29412
Non-polymers00
Water00
1
A: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0251
Polymers17,0251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.404, 110.048, 166.234
Angle α, β, γ (deg.)90.000, 90.205, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MAP kinase phosphatase 5 / MKP-5


Mass: 17024.502 Da / Num. of mol.: 12 / Fragment: CD domain (UNP residues 320-466) / Mutation: I445A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
Has protein modificationN

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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: 4.76 Å3/Da / Density % sol: 74.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M imidazole, pH 8.0, 2.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2025
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.502→166.233 Å / Num. obs: 46689 / % possible obs: 96 % / Redundancy: 6.9 % / Biso Wilson estimate: 84.48 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.5
Reflection shellResolution: 3.502→3.52 Å / Rmerge(I) obs: 1.456 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2456 / CC1/2: 0.403

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.502→166.23 Å / SU ML: 0.4308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9102
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2446 2176 4.67 %
Rwork0.2114 44450 -
obs0.213 46626 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.17 Å2
Refinement stepCycle: LAST / Resolution: 3.502→166.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14177 0 0 0 14177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314488
X-RAY DIFFRACTIONf_angle_d0.629419585
X-RAY DIFFRACTIONf_chiral_restr0.03622148
X-RAY DIFFRACTIONf_plane_restr0.01582554
X-RAY DIFFRACTIONf_dihedral_angle_d16.83115374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.502-3.580.32841030.32362915X-RAY DIFFRACTION99.87
3.58-3.650.3231140.31122382X-RAY DIFFRACTION91.06
3.67-3.750.35451220.27932324X-RAY DIFFRACTION91.51
3.75-3.850.29971790.2542822X-RAY DIFFRACTION100
3.85-3.970.3058770.24322119X-RAY DIFFRACTION72.09
3.97-4.10.2451340.22192883X-RAY DIFFRACTION100
4.1-4.240.22921050.21272929X-RAY DIFFRACTION100
4.24-4.410.21531060.21512911X-RAY DIFFRACTION99.93
4.41-4.610.23451500.1892906X-RAY DIFFRACTION100
4.61-4.860.21481920.16532802X-RAY DIFFRACTION100
4.86-5.160.21311650.1782843X-RAY DIFFRACTION100
5.16-5.560.22681340.20052935X-RAY DIFFRACTION100
5.56-6.120.28381540.22472911X-RAY DIFFRACTION100
6.12-70.28551320.22712895X-RAY DIFFRACTION100
7.01-8.820.24971470.19392916X-RAY DIFFRACTION100
8.82-166.230.19121620.17172957X-RAY DIFFRACTION98.67

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