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- PDB-7y4d: Crystal structure of DUSP10 mutant_S95A -

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Basic information

Entry
Database: PDB / ID: 7y4d
TitleCrystal structure of DUSP10 mutant_S95A
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE / Dual specificity protein phosphatase 10 / MAP kinase phosphatase 5
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 / negative regulation of JNK cascade / negative regulation of stress-activated MAPK cascade / positive regulation of regulatory T cell differentiation / dephosphorylation / mitogen-activated protein kinase p38 binding / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / 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 / cytosol / 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 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 / Tyrosine specific protein phosphatases domain profile. / 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: 2.18 Å
AuthorsHu, I.C. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of DUSP10 mutant_S95A
Authors: Hu, I.C. / Lyu, P.C.
History
DepositionJun 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)34,2152
Polymers34,2152
Non-polymers00
Water1,47782
1
A: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,1081
Polymers17,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,1081
Polymers17,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.270, 42.649, 56.526
Angle α, β, γ (deg.)74.320, 82.350, 63.860
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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: 17107.568 Da / Num. of mol.: 2 / Mutation: S95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22.5% (w/v) PEG 3000, 100 mM Tris base /Hydrochloric acid, 200 mM Calcium acetate
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→30 Å / Num. obs: 15595 / % possible obs: 94.3 % / Redundancy: 2 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 34.111
Reflection shellResolution: 2.18→2.26 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5.264 / Num. unique obs: 15568

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zzw

1zzw


Resolution: 2.18→24.97 Å / SU ML: 0.2298 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.0998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 1557 10 %
Rwork0.1801 14011 -
obs0.185 15568 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 2.18→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 0 82 2488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322458
X-RAY DIFFRACTIONf_angle_d1.36163324
X-RAY DIFFRACTIONf_chiral_restr0.0655366
X-RAY DIFFRACTIONf_plane_restr0.0123434
X-RAY DIFFRACTIONf_dihedral_angle_d7.9964324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.250.28251370.24951230X-RAY DIFFRACTION91.26
2.25-2.330.30221340.23711198X-RAY DIFFRACTION88.74
2.33-2.420.2881460.20891308X-RAY DIFFRACTION96.74
2.42-2.530.25061480.1991337X-RAY DIFFRACTION97.12
2.53-2.660.25361440.19451297X-RAY DIFFRACTION96.91
2.66-2.830.23811480.20271333X-RAY DIFFRACTION96.36
2.83-3.050.24361470.20751324X-RAY DIFFRACTION96.46
3.05-3.350.2731430.20441285X-RAY DIFFRACTION95.84
3.35-3.840.18971260.16831133X-RAY DIFFRACTION83.1
3.84-4.820.19131390.1381254X-RAY DIFFRACTION92.8
4.83-24.970.21951450.16311312X-RAY DIFFRACTION96.3
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.322601635451.84960458214-1.171886376435.86991140846-2.143365675484.705716933670.00606812499339-0.380307875464-0.4873455645620.215716206478-0.370798305892-1.207697649360.6385638144791.11843854630.3194759744030.2991517382270.09078542887060.005076478382010.5572116424750.07226153473480.51809317208610.62480926710.253003789719-4.43168887144
21.436188831910.4271868887490.04061322101642.88765660274-1.798245476793.51374607433-0.104769746933-0.440113044371-0.3690214150260.0460142028212-0.0644155356983-0.526456833896-0.2607567991591.10729486530.2852145314750.391129749558-0.02474994512380.0008549906281390.5620881704760.03784124043620.3444594035111.6573923156-0.1153418915722.50659713894
31.355385035851.39253473787-0.7214167939163.41545979717-1.477306294613.417454230860.112362247827-0.4469795669520.05794816114250.54159716856-0.342014147249-0.365407554809-0.2568907316720.3603122211530.1412073753680.563779663177-0.1377246266650.007328551891480.416199157694-0.006376528734740.2585412377716.172139084420.016204808363510.9594407909
43.650602233381.879458948041.085337154152.69367974512-0.1472722125055.39788672260.2268343495840.0207846552824-0.9837175442830.0926549735250.1537406282180.3237250061421.26566528112-0.290140647829-0.217765529740.755539064338-0.193722281252-0.02507533770660.461103315146-0.05751353298810.482947268578-8.65049894583-10.08588320064.66056438411
52.617402884072.35550336974-0.3367334529023.40524672493-0.846026547533.253760906090.217053915681-0.3197539769670.8138505080040.714935163086-0.10339237320.759707435214-0.599874001806-0.307637362996-0.1745725745930.448759724288-0.00873973300330.1131016836670.360529960331-0.01033021527770.375079830299-4.591014250017.176423095563.76345064664
62.021472937971.06325910045-0.2415307885362.73430508661-1.426191505194.313254335180.143300038331-0.2539202223330.1089574111740.2273596121680.04232477277340.1124003998120.1018427974590.0745417151661-0.02059682762170.269394156502-0.001636813002920.0323580845590.244494968923-0.03721942292090.256114156525-0.4021328799980.254498144463-1.1248081207
73.534592268851.36664134761-0.3951296896761.86842131059-1.181309247455.28185829305-0.1837848092980.294540100510.0409196840876-0.3896699082020.2220306601750.1096404353450.669245455395-0.010356508898-0.01597707101710.392393922857-0.01690475816970.0282994220240.315941359591-0.03275802240220.277912102911-1.09361969586-2.01181145635-11.2859821416
82.82983827973-0.133252473113-0.1938210654674.55256361917-1.915274118934.78276765282-0.09050505674151.117918444720.0736562927503-0.5275932397790.1856705687970.9332672128470.32604060225-0.959433224244-0.3385367047220.319875803146-0.150146196780.01640967220060.5915055124580.08420029309480.462985544513-14.4825919096-0.509416169738-6.88740504885
91.486712953781.72328674715-1.468654230612.69905910562-1.429937182274.33720067543-0.3608774052380.219255759646-0.302022005884-0.6114953465270.0202481767097-0.2490859643780.4787833166760.498203604650.1991739645660.426430377037-0.02783434602130.003529930687330.4241203095580.01201881181950.34728537668411.48319206217.69878491952-30.0123833191
100.5656435565530.117356642991-0.873299770035.53832394711-1.386318574254.59086056261-0.3281729392940.4822673838930.348157125337-0.1742425434840.763123119410.543143971633-0.483765208126-0.209045867117-0.1395914224560.405935865679-0.0402664778944-0.08495453130680.3776963668670.04339709017780.334672534282.4917430427619.6103587167-27.2975723273
112.039716639640.902410333474-1.061263785733.28654774895-0.8463421157794.54014406425-0.303340340950.3218334487530.173025135987-0.397718801770.2002964009380.2740593967470.05361211551310.244570237386-0.02443505200320.25845446798-0.0148699315828-0.01742970269480.3266145636590.03141874282860.2719889051716.1484742900914.4143119415-22.7269041972
124.71531504448-0.458139861035-1.131143965556.35097380622-0.6906743674966.19595718603-0.193036609677-0.8358468919420.2031920677430.7278685773240.4295857884330.4517961024930.00238595910170.0939427925732-0.05772445685570.481296866365-0.04751652550290.02413985208610.339327390510.005382890427450.3007540954175.3262511945515.608556198-10.5526536293
130.2460875234990.606613292214-0.3630398530231.58142994892-0.9990262088260.5912168958290.0457934755941-0.2729009621040.4184675031710.371062482412-0.0154607295432-0.337502066227-0.6431668436641.394285959570.1914890617320.78060719626-0.0832418403107-0.1767769139650.8249616327690.03641876103880.51593221189615.832204740318.4231304762-16.2102370234
146.816319860070.823778287926-3.971905527234.55190630945-1.988598888686.75381598354-0.523563097966-0.4328761504510.3675308098460.2748045081680.1758457913370.556233175189-1.32777009281-0.166322973512-0.3329665202940.7830669275840.05392127859740.05079305161220.190003488749-0.04891728151210.464834210629-0.36793243317426.7161216552-15.9028456112
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 8 )AA1 - 81 - 8
22chain 'A' and (resid 9 through 27 )AA9 - 279 - 27
33chain 'A' and (resid 28 through 54 )AA28 - 5428 - 54
44chain 'A' and (resid 55 through 65 )AA55 - 6555 - 65
55chain 'A' and (resid 66 through 82 )AA66 - 8266 - 82
66chain 'A' and (resid 83 through 108 )AA83 - 10883 - 108
77chain 'A' and (resid 109 through 130 )AA109 - 130109 - 130
88chain 'A' and (resid 131 through 149 )AA131 - 149131 - 149
99chain 'B' and (resid 1 through 54 )BB1 - 541 - 54
1010chain 'B' and (resid 55 through 81 )BB55 - 8155 - 81
1111chain 'B' and (resid 82 through 108 )BB82 - 10882 - 108
1212chain 'B' and (resid 109 through 123 )BB109 - 123109 - 123
1313chain 'B' and (resid 124 through 130 )BB124 - 130124 - 130
1414chain 'B' and (resid 131 through 149 )BB131 - 149131 - 149

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