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- PDB-7y4b: Crystal structure of DUSP10 mutant_D59A -

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Basic information

Entry
Database: PDB / ID: 7y4b
TitleCrystal structure of DUSP10 mutant_D59A
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 / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / Signaling by MAPK mutants / negative regulation of oligodendrocyte differentiation / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / negative regulation of JNK cascade / JUN kinase binding / positive regulation of regulatory T cell differentiation / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / 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 / 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 / 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: 1.86 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_D59A
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)34,1592
Polymers34,1592
Non-polymers00
Water3,027168
1
A: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0801
Polymers17,0801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0801
Polymers17,0801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.230, 41.584, 56.826
Angle α, β, γ (deg.)96.030, 100.440, 117.450
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: 17079.559 Da / Num. of mol.: 2 / Mutation: D59A
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 / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 48.13 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22.5%(w/v) PEG 3000, 100mM Tris base/Hydrochloric acid, 200mM Calcium acetate
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 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: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 23176 / % possible obs: 88.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 27.748
Reflection shellResolution: 1.86→1.94 Å / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 6.65 / Num. unique obs: 23130 / % possible all: 88.3

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Processing

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

1zzw


Resolution: 1.86→24.76 Å / SU ML: 0.1941 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.0842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 1986 8.59 %
Rwork0.1836 21144 -
obs0.1876 23130 87.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.58 Å2
Refinement stepCycle: LAST / Resolution: 1.86→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 168 2570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182454
X-RAY DIFFRACTIONf_angle_d1.22873318
X-RAY DIFFRACTIONf_chiral_restr0.0633366
X-RAY DIFFRACTIONf_plane_restr0.0103432
X-RAY DIFFRACTIONf_dihedral_angle_d7.1759324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.32731140.24341332X-RAY DIFFRACTION76.11
1.91-1.960.31221610.22521589X-RAY DIFFRACTION92.94
1.96-2.020.23681450.20241582X-RAY DIFFRACTION92.7
2.02-2.080.22941490.20211557X-RAY DIFFRACTION91.08
2.08-2.160.24561470.18941574X-RAY DIFFRACTION91.54
2.16-2.240.2281520.1971582X-RAY DIFFRACTION91.31
2.24-2.350.26481390.19961502X-RAY DIFFRACTION88.42
2.35-2.470.26841450.20431553X-RAY DIFFRACTION90.22
2.47-2.620.27511380.19791539X-RAY DIFFRACTION89.92
2.62-2.830.22731510.19781509X-RAY DIFFRACTION88.11
2.83-3.110.23941390.20341523X-RAY DIFFRACTION89.26
3.11-3.560.24611430.17991525X-RAY DIFFRACTION87.79
3.56-4.480.19581190.14481219X-RAY DIFFRACTION71.86
4.48-24.760.19031440.16851558X-RAY DIFFRACTION90.77
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)
13.768093876430.008854208679181.238527284394.551365081371.374207202435.6801736659-0.197147732572-0.330065496471-0.07090739979310.8088767281880.329012849635-0.2230529901410.480608010076-0.372248899848-0.106195962680.443704501148-0.103399696932-0.01129449681690.3151961589270.01780122837310.235036478322-6.5260797818-13.5993525315-9.98466514273
2-0.0144367251822-0.033573696613-0.02805764669681.13265458421.0762250850.9394757395310.313859165941-0.77027752081-0.116258691231-0.33141844158-0.508636100750.9934784225410.632214315958-1.098423251890.2061715426840.70337516984-0.1372743000170.08880497755310.71274128493-0.01971332562780.582012426862-17.1502883041-15.996408354-16.4463574375
34.74845959790.842241537793.435824672551.82990748031.464852774045.94914911937-0.0467995784036-0.475054968168-0.5195745484850.4277002425250.076084938743-0.5626957810741.32691801947-0.0118712662497-0.4773020886750.5732728409270.0378681427896-0.109283109310.312280931731-0.001999954449090.450412668852-1.40387293312-25.2605997412-14.4520587704
42.146645407090.1799160327180.3366763452546.688498223422.546529575014.66844172347-0.124368216211-0.1225691498320.61119331541-0.694542691214-0.007711204586450.304885445274-0.993726045971-0.7306388026740.268577403640.4065596812760.169649271281-0.06928384280490.389246558998-0.02918539781540.383043410549-9.768544593233.09497647317-4.89187666222
52.251727567030.879146326233-0.6615662504092.698853410871.739553569364.9489677664-0.294081906652-0.1436877659530.469925269765-0.102156080770.04518128108070.346380794325-0.434462205054-0.9994458240830.2024077134790.2597753036490.125669272089-0.04421579310250.369655152422-0.0311733533110.269011524259-9.373400920343.34580219741.83983441018
62.350066806971.411710518181.560643310893.080067076641.788025297084.033315549150.124483572145-0.3844827515730.07320491634920.150347049001-0.4667536701280.6027567647140.0304325209279-0.9670583633510.2878108512170.268572433348-0.01093601868490.03285040148550.440408236319-0.05911864550430.32269773232-12.1555900519-1.865919891455.89255500159
72.601440927391.243919589261.052796755544.290167344721.429274066764.631238033050.206233413667-0.2253792943590.09241127071840.512593993544-0.3980324835210.3971922022560.117107881564-0.5092142694530.1877445544430.311447764602-0.05005748270270.02594754539790.312944524246-0.01098092174020.214525939522-6.074628686233.7314388131813.3107410968
83.307296343710.329835127110.6646769875265.579253565281.328466491725.767391927110.2877955546520.5939007015830.9672574805470.07119355191390.275084841165-0.627859627482-1.336356594350.145733646466-0.1552817344220.480856521372-0.0675190161490.0762636008570.3661288635210.05066850374610.4196927739519.1921009029510.7077281025.52246950226
92.899461645021.823300878530.872108952733.370110806141.556858778753.409128248590.478176431959-0.0259400945021-0.7610629311030.736070559386-0.0239663794918-0.5122575153660.7662592680690.1833798127-0.2264595080260.3546215863370.0380294322997-0.05411620861120.250823371030.008842800095820.2895971637653.96898171349-5.682235524044.60570249862
102.408106514460.5203664358810.2310915170782.122769018821.570021690355.20595359531-0.00174372169358-0.0435467181459-0.0263934858032-0.144111522328-0.0489970753511-0.0384564209007-0.320747045205-0.247176021367-0.03502316365220.2383861718360.0451319426208-0.008813559040810.1892845321460.01683779405550.2504501949710.1721060173561.41312737719-0.509398900885
115.617792757980.8324941849890.4905569714733.83114488221.358288687276.794920481350.06884213795390.657893513394-0.217263772293-0.260774622161-0.0122421741975-0.131582614817-0.2788540039290.0867015721318-0.1171704124920.311876479231-0.03575975071520.02553037812080.2796050149620.001099168016760.2746065039262.52527935806-0.0831856757655-12.3977833002
121.845444632991.317186411830.9383308418961.434986459561.513104884591.95197885586-0.2491027437580.1873066315410.978983427111-0.7507943072640.143825946954-0.0417873068332-1.34045094569-0.06832157505810.2349317982880.591791111503-5.50970989601E-5-0.0680129881420.3003074416060.03008603490610.464399797417-0.89019517886810.2315254543-7.29128031719
133.126457105490.379573125037-0.00617622621925.078861807873.198026671016.048573943180.04484456503840.314360852087-0.152023330477-0.157389166490.335399712844-0.682892751787-0.304381594371.16461310456-0.4220750192810.303575836541-0.1193270915780.06740855559750.537155764745-0.1144564804570.34208744551514.44610606461.45981442306-5.81150269409
143.511649152512.639664764722.215966098862.00993482631.176131422225.14454017722-0.4064235691380.04977156088740.965525121435-1.02223812992-0.3553247666071.49682066299-0.478534991427-1.134291340850.2941297244490.4333425106920.11778607929-0.1483329127550.406739124289-0.1039583111820.580519672183-13.4019356688-3.65717878795-19.8188943753
152.137350302461.079467826371.885668606922.33036688881.693548751144.566928305490.122209874420.201293890840.325735874428-0.415531297408-0.1891052934860.556980581418-0.863043231945-0.3388304819740.3080046535090.4288371679190.0764219150798-0.03625624302820.3615556970120.000464202374380.347983080378-12.7002630465-3.10695788109-26.6794760081
161.743181083950.9632064991181.072692561811.963266621281.661843026613.45640962718-0.3791727257020.247927859470.209421310041-0.5213004593090.226343257262-0.145342660398-0.8683288363180.3560680214550.08573389197480.498419922087-0.1034064112110.006979401007770.2812582906330.01264648933280.249549077652-8.98219181447-8.17607183996-34.5054725506
172.580752741990.4687543753641.593782648353.126440750221.189871674385.149049140410.08576136605290.0177844039916-0.5436965059750.472118644810.178205408008-0.0753768150730.991754034815-0.870920030191-0.2205740136660.533391017037-0.1146273895510.03070155005050.397779236175-0.05178295905640.364816189749-10.1233019372-26.1063650681-27.7779385101
182.112333079212.625109431161.317762680346.209549423011.630145280433.68348396866-0.4891232669160.659194283549-0.519141921944-0.5501753496990.931375040102-1.25410489181-0.2115000041891.01547885834-0.2891151148330.378058470032-0.07912203179810.06978146834990.431780762123-0.09582490805580.3838915727641.80689209198-13.3701612708-25.9646149988
192.290282663790.7599539310781.657182869552.81651934111.323159024685.022987621180.128855629660.0542500180083-0.269393902949-0.1011815086290.135129699447-0.1668018976640.000654265953126-0.0990910556256-0.09222131748810.270806358648-0.01699757216730.04090867369750.267039434204-0.009165262808640.279835159453-6.93565793894-13.1504427806-21.9178487107
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 109 through 123 )BB109 - 123109 - 123
22chain 'B' and (resid 124 through 130 )BB124 - 130124 - 130
33chain 'B' and (resid 131 through 149 )BB131 - 149131 - 149
44chain 'A' and (resid 1 through 8 )AA1 - 81 - 8
55chain 'A' and (resid 9 through 21 )AA9 - 219 - 21
66chain 'A' and (resid 22 through 35 )AA22 - 3522 - 35
77chain 'A' and (resid 36 through 54 )AA36 - 5436 - 54
88chain 'A' and (resid 55 through 65 )AA55 - 6555 - 65
99chain 'A' and (resid 66 through 82 )AA66 - 8266 - 82
1010chain 'A' and (resid 83 through 108 )AA83 - 10883 - 108
1111chain 'A' and (resid 109 through 123 )AA109 - 123109 - 123
1212chain 'A' and (resid 124 through 130 )AA124 - 130124 - 130
1313chain 'A' and (resid 131 through 149 )AA131 - 149131 - 149
1414chain 'B' and (resid 1 through 8 )BB1 - 81 - 8
1515chain 'B' and (resid 9 through 27 )BB9 - 279 - 27
1616chain 'B' and (resid 28 through 54 )BB28 - 5428 - 54
1717chain 'B' and (resid 55 through 65 )BB55 - 6555 - 65
1818chain 'B' and (resid 66 through 82 )BB66 - 8266 - 82
1919chain 'B' and (resid 83 through 108 )BB83 - 10883 - 108

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