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- PDB-7y4e: Crystal structure of DUSP10 mutant_N130A -

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Basic information

Entry
Database: PDB / ID: 7y4e
TitleCrystal structure of DUSP10 mutant_N130A
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 / negative regulation of stress-activated MAPK cascade / 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 / 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 / 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: 1.93 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_N130A
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)34,1612
Polymers34,1612
Non-polymers00
Water2,342130
1
A: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0811
Polymers17,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0811
Polymers17,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.420, 41.156, 55.742
Angle α, β, γ (deg.)95.760, 99.680, 117.230
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: 17080.545 Da / Num. of mol.: 2 / Mutation: N130A
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.: 130 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27.5% (w/v) PEG 3000, 100 mM Tris base /Hydrochloric acid, 175mM 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: Dec 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 20095 / % possible obs: 90.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 30.52 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.201
Reflection shellResolution: 1.93→2.01 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.159 / Num. unique obs: 20048

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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: 1.93→26.91 Å / SU ML: 0.2204 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.6436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 1983 9.89 %
Rwork0.1951 18065 -
obs0.1988 20048 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.67 Å2
Refinement stepCycle: LAST / Resolution: 1.93→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 130 2532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01422454
X-RAY DIFFRACTIONf_angle_d1.2853318
X-RAY DIFFRACTIONf_chiral_restr0.0661366
X-RAY DIFFRACTIONf_plane_restr0.0114432
X-RAY DIFFRACTIONf_dihedral_angle_d7.7869324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.27351030.2516989X-RAY DIFFRACTION67.16
1.98-2.030.28391480.24581177X-RAY DIFFRACTION83.7
2.04-2.090.32311350.24371326X-RAY DIFFRACTION90.13
2.09-2.160.27731660.22641352X-RAY DIFFRACTION93.82
2.16-2.240.26041410.22971371X-RAY DIFFRACTION95.58
2.24-2.330.28251500.21721401X-RAY DIFFRACTION95.27
2.33-2.440.2511620.22091394X-RAY DIFFRACTION95.69
2.44-2.560.32111370.21031354X-RAY DIFFRACTION95.39
2.56-2.720.26491560.20681379X-RAY DIFFRACTION94.35
2.72-2.930.27441510.20481361X-RAY DIFFRACTION93.56
2.93-3.230.24581440.20471331X-RAY DIFFRACTION91.96
3.23-3.690.2081330.17411254X-RAY DIFFRACTION87.12
3.7-4.650.16971290.15391213X-RAY DIFFRACTION82.79
4.66-26.910.20911280.18791163X-RAY DIFFRACTION80.79
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)
10.6217807661570.2479337832170.473038372310.642173234660.5663448681281.436377990090.0307724278685-0.1601992815040.158810461097-0.0341585852355-0.3302540288350.158270869603-0.0301301778982-0.8133928053160.0009103308458370.31398226492-0.0142825928621-0.006889573361070.500570721489-0.0363968647590.29760217112-8.63503169194-0.5899665930626.60188052936
21.08188200577-0.471885008840.2229881531990.3300998090390.3918795046752.252161558080.07495602611610.1857584541160.03722195051870.4222610586370.174057407501-0.3387126753570.2235586685040.160524907498.80526261542E-50.339309013417-0.0272950202175-0.03512477002720.3374938646470.003462518904480.3206467365586.37601144865-2.258732291675.08325590183
31.122654328890.9916793285610.9470068349871.125252430031.510455655052.578404108-0.05330805893630.0617408195475-0.0302211227571-0.117440821990.0213091964622-0.0389025646079-0.165421166603-0.100439583164-0.0004814063971840.26760357409-0.0188161210889-0.003505560930720.272587573450.03222719542650.2592068172380.783022181878-1.02379786544-4.99054682612
40.27776419448-0.3109127591760.2462059179740.707528593301-1.289342557944.646419014330.1894555153660.655073568245-0.2081642389230.02554505584670.0975298707341-0.784569120394-0.5800878848431.245061718160.08037348235230.20036268997-0.04894056720740.01900362952110.49976315846-0.1264389611390.45036813453714.5652926855-1.45710732173-5.67444852396
50.4127893630030.457739591569-0.6945108813990.773266324826-1.219189955922.32357427760.1114057265650.1761856837990.0543859552214-0.221629269019-0.3063443225390.54300494053-0.94539985618-0.339146820017-0.128211124190.4238985732520.16184282959-0.05655587358370.347256270296-0.09513314221190.409399534513-13.0047065421-8.34210879107-22.958321604
60.3307487379840.1376885454950.1359103810660.08310253036070.05509855053870.0807516231814-0.3060596027160.01760836319370.179451525411-0.2965278524260.275958842230.222174162943-0.898848350869-0.02346179044310.04022133796380.8445854206780.135599435223-0.03557369125510.2848867436750.01128667277940.352891086526-8.98983635046-4.05884042827-29.0708130271
70.273358306502-0.189749506637-0.4082360727840.1598286881710.3394625817270.675534880124-0.03399738973120.241108678641-0.03100063945710.02443008391630.02357144542690.106999596725-0.554582142893-0.135624978758-0.0006376323175520.4368326910610.03521399174580.01718202763420.329707009291-0.02110715252630.361308182535-10.2454364308-12.5294131112-36.0924243024
80.05372168057730.06444588440150.0950162757540.09997501631390.0807333908030.1321833638880.5925296666440.400891077913-0.383051603410.648595527010.1933688624880.335314903110.710254299573-0.4800612026230.04318102147070.521903155118-0.0785583035541-0.03929278231280.4072887368240.06537966963210.42192210875-10.5601609971-28.4728421648-27.2854750314
90.53004103243-0.05064235195570.4954758227990.423357931263-0.1177176592630.471107714415-0.4557592090220.277714094695-0.14635749229-0.5099984949330.928312234953-0.774515023747-0.2461544491240.7825465374850.03756234481510.423179753937-0.03849479824290.04723824516910.362730250373-0.04310160479260.3516451299881.91722020196-16.2998879565-25.7049174312
100.262169216983-0.0716652289916-0.04105046088880.02307343305970.01529856244480.02585536156660.154113056876-0.340081413579-0.04172032778920.241316258855-0.0472513717009-0.0883093326542-1.05605174435-0.0653436191856-0.01305921722270.549509870606-0.125002015870.04047055997070.360838144888-0.001677094878860.34391381367-5.92238430923-8.87015659088-26.9013700024
110.1316405549690.012270032609-0.2767098343340.4718065001310.4997361653420.8128294045640.219999919074-0.103266822802-0.3137486391360.0132392011286-0.131788172360.009917375062830.105848960771-0.2356721896720.0002271800397660.2421079694980.01098940489320.009973168200670.324618769029-0.01327293212920.32882190682-7.20352267799-18.365219506-19.7859980167
120.230868540385-0.1419475548590.1644903257230.1546417327480.09564569089290.470007524745-0.0243743436552-0.6940692038150.1035922211910.573046970878-0.0771875981101-0.113716739838-0.0337224019011-0.45845185738-0.005329214246370.427620246672-0.0393830814962-0.01036088342230.319900554656-0.001032118818920.363711412684-6.4684372969-16.4113980862-9.74787439058
130.103500228734-0.01397541287580.08942280234650.0417028982380.02101655613940.0705737883789-0.0103924133114-0.121241605725-0.0300905821232-0.467251680912-0.2421600944030.3179005220590.765956784772-1.06745640864-0.0005687904061070.517512778031-0.01453802235650.1320933068480.612407636676-0.1025511713460.490389808544-16.3992671543-17.9439011453-15.8069751187
140.204007803879-0.01419207158480.2309884237510.111666624467-0.1483898924840.363312664049-0.0794600625243-0.04715328555630.1176052145050.2221097775210.116127910639-0.162852185640.5890177625070.07754583076050.0008421911022750.504904302546-0.00193520435872-0.1010194024660.303860411010.03534625335960.38788135561-1.15895013398-28.0464313038-14.3245971303
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 54 )AA1 - 541 - 54
22chain 'A' and (resid 55 through 81 )AA55 - 8155 - 81
33chain 'A' and (resid 82 through 130 )AA82 - 13082 - 130
44chain 'A' and (resid 131 through 149 )AA131 - 149131 - 149
55chain 'B' and (resid 1 through 21 )BB1 - 211 - 21
66chain 'B' and (resid 22 through 35 )BB22 - 3522 - 35
77chain 'B' and (resid 36 through 54 )BB36 - 5436 - 54
88chain 'B' and (resid 55 through 65 )BB55 - 6555 - 65
99chain 'B' and (resid 66 through 82 )BB66 - 8266 - 82
1010chain 'B' and (resid 83 through 89 )BB83 - 8983 - 89
1111chain 'B' and (resid 90 through 108 )BB90 - 10890 - 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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