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- PDB-5f59: The crystal structure of MLL3 SET domain -

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Basic information

Entry
Database: PDB / ID: 5f59
TitleThe crystal structure of MLL3 SET domain
ComponentsHistone-lysine N-methyltransferase 2C
KeywordsTRANSFERASE / Histone methylation / histone methyltransferase / SET domain
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / acyltransferase activity / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / response to electrical stimulus ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / acyltransferase activity / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / response to electrical stimulus / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / methylation / histone binding / transcription coactivator activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / FY-rich, N-terminal ...Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PHD-zinc-finger like domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Beta Complex / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å
AuthorsLi, Y. / Lei, M. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08010201 China
CitationJournal: Nature / Year: 2016
Title: Structural basis for activity regulation of MLL family methyltransferases.
Authors: Li, Y. / Han, J. / Zhang, Y. / Cao, F. / Liu, Z. / Li, S. / Wu, J. / Hu, C. / Wang, Y. / Shuai, J. / Chen, J. / Cao, L. / Li, D. / Shi, P. / Tian, C. / Zhang, J. / Dou, Y. / Li, G. / Chen, Y. / Lei, M.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4533
Polymers18,0041
Non-polymers4502
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.056, 129.056, 129.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Histone-lysine N-methyltransferase 2C / Lysine N-methyltransferase 2C / Homologous to ALR protein / Myeloid/lymphoid or mixed-lineage ...Lysine N-methyltransferase 2C / Homologous to ALR protein / Myeloid/lymphoid or mixed-lineage leukemia protein 3


Mass: 18003.604 Da / Num. of mol.: 1 / Fragment: MLL3 SET domain (UNP RESIDUES 4757-4910)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2C, HALR, KIAA1506, MLL3 / Plasmid: pET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q8NEZ4, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.97 Å3/Da / Density % sol: 75.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl, pH8.5, 3M NaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U11.2818
SYNCHROTRONSSRF BL17U20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 31, 2014
ADSC QUANTUM 315r2CCDMay 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28181
20.97931
ReflectionRedundancy: 13.3 % / Number: 72976 / Rmerge(I) obs: 0.204 / Χ2: 2.2 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 5503 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
9.215010.0813.89610.5
7.329.2110.0932.50312.5
6.47.3210.1392.0912.3
5.816.410.1632.18312.8
5.45.8110.1572.55813.1
5.085.410.1642.27413.1
4.825.0810.1712.42713.4
4.614.8210.152.39913.3
4.444.6110.1582.30513.4
4.284.4410.172.35913.7
4.154.2810.1712.22613.6
4.034.1510.2192.09913.7
3.924.0310.2372.05513.8
3.833.9210.2742.19713.7
3.743.8310.2921.92513.8
3.663.7410.3191.88314
3.593.6610.3411.76313.7
3.523.5910.4161.6414.2
3.463.5210.4961.66213.8
3.43.4610.5631.67113.9
ReflectionResolution: 2.8→50 Å / Num. obs: 9555 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 39.44 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.044 / Rrim(I) all: 0.142 / Χ2: 2.18 / Net I/av σ(I): 31.559 / Net I/σ(I): 9.1 / Num. measured all: 96884
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.910.60.5379040.9360.1690.5571.414100
2.9-3.0210.60.3929330.9710.1250.4121.469100
3.02-3.1510.60.2749410.9790.0880.2881.53100
3.15-3.3210.60.2129270.9860.0680.2231.635100
3.32-3.5310.40.1689340.9920.0540.1761.888100
3.53-3.810.40.1259600.9950.0410.1322.155100
3.8-4.1810.20.1059370.9960.0350.1112.682100
4.18-4.799.70.0969610.9950.0330.1023.395100
4.79-6.039.50.0999890.9960.0340.1053.08100
6.03-5090.06810690.9970.0240.0722.71299.2

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
170.28285.2660.782N46.651
270.5986.46561.613CA47.811
370.2887.76160.868CB45.71
471.34588.08159.984OG46.741
569.85386.46562.918C47.621
670.45586.69263.962O49.871
768.55186.22562.859N47.281
867.77686.07764.069CA50.511
966.39385.54563.736CB56.621
1065.66585.40764.948OG72.041
1168.47185.12665.045C48.561
1268.44585.31466.262O42.941
1369.08884.09864.474N52.711
1469.8183.08865.219CA53.331
1570.07881.84564.34CB55.471
1671.06282.00663.161CG60.141
1770.49782.66761.886CD54.611
1869.65383.54361.942OE152.541
1971.00982.25760.734NE252.661
2071.0883.69765.806C53.311
2171.31983.51667.005O51.431
2271.84584.44764.981N53.121
2373.08685.1465.425CA53.711
2473.82185.9264.318CB61.231
2573.98885.27762.973CG73.831
2674.02883.88662.835CD185.231
2774.18283.29761.589CE196.751
2874.32384.11460.463CZ99.431
2974.48183.5259.23OH108.041
3074.3185.50460.578CE285.291
3174.15586.07261.829CD275.51
3272.78686.16466.499C46.671
3373.54886.33967.448O43.911
3471.68486.86866.309N41.631
3571.28587.88267.237CA39.741
3670.07688.65166.681CB38.681
3769.4189.61867.646CG37.641
3870.33490.75968.026CD37.881
3969.59991.87268.605NE38.871
4068.70191.74769.573CZ38.591
4168.42390.54770.056NH137.381
4268.0892.82270.047NH239.981
4371.02587.24468.603C40.981
4471.54187.70669.621O40.91
4570.26486.15568.621N44.081
4669.91385.50769.884CA46.571
4769.17484.18469.63CB48.391
4868.06983.82770.623CG45.081
4967.03382.93469.942CD44.781
5066.21483.70168.895CE46.781
5166.29283.11367.519NZ45.781
5271.19485.26370.659C46.871
5371.24885.60171.842O43.881
5472.20984.71669.958N46.611
5573.48384.29470.54CA46.131
5674.34183.47169.571CB52.31
5775.05282.31970.296CG72.331
5876.62781.60469.707SD93.021
5976.71180.0470.615CE88.111
6074.2585.49871.02C43.771
6174.48585.64472.218O46.741
6274.6286.37470.094N40.821
6375.26287.64570.44CA37.481
6475.03488.67669.348CB36.211
6575.64590.01769.672CG32.41
6675.13691.0768.734CD30.551
6774.26691.9769.54CE29.921
6874.99392.23170.806NZ28.61
6974.788.22771.706C36.251
7075.40988.83572.49O36.691
7173.41188.04471.903N37.341
7272.78888.62473.061CA41.221
7371.26788.94972.805CB44.451
7471.1390.35772.507OG142.11
7570.28488.53773.98CG245.861
7673.23388.01174.421C41.831
7772.83488.51575.478O42.541
7874.08786.97374.396N43.081
7974.75886.48975.632CA49.681
8074.77884.98575.75CB47.841
8173.43284.47176.114CG52.531
8272.46284.84675.033CD61.11
8372.63384.35473.892OE168.851
8471.56185.66775.312OE268.711
8576.17786.97575.808C55.631
8676.63487.26676.928O60.521
8776.88287.07374.704N55.861
8878.24187.47574.812CA59.251
8979.10986.63773.836CB79.321
9078.59385.12773.519CG101.091
9177.62484.76972.608CD1100.41
9277.4683.39972.578NE1105.851
9378.32982.81473.463CE2121.081
9479.07483.86174.081CD2121.871
9580.04283.51475.051CE3129.941
9680.24182.13775.367CZ3122.841
9779.4881.12874.729CH2125.011
9878.52581.44173.781CZ2124.351
9978.43889.0574.832C53.891
10078.48289.77173.831O52.941
10178.47889.5876.036N47.671
10279.27390.76176.289CA43.451
10378.591.77577.148CB42.41
10477.96993.03576.457CG36.651
10576.793.58277.124CD29.321
10675.48892.79176.636CE26.251
10775.79691.87475.481NZ22.251
10880.51490.18877.026C42.791
10981.12390.8277.896O39.821
11080.84788.94676.677N43.541
11182.14788.35676.953CA42.781
11282.06686.84876.908CB43.751
11381.04486.39377.757OG54.561
11483.05288.7475.825C42.511
11584.17488.27175.749O46.651
11682.54389.55974.917N41.091
11783.29489.97573.757CA37.911
11882.34790.18772.562CB43.261
11981.47588.9672.242CG45.491
12081.83287.81172.547OD148.21
12180.3389.20871.605ND241.731
12284.0791.26274.032C35.11
12384.99591.58973.299O34.181
12483.72391.98375.096N32.21
12584.15893.37775.22CA30.441
12683.00394.32874.848CB28.751
12782.88294.43673.347CG128.121
12881.68193.82575.402CG229.011
12984.74293.79576.569C32.291
13084.25393.33577.599O34.551
13185.79994.63176.523N35.441
13286.40995.39777.645CA36.651
13387.92795.53477.494CB45.311
13488.71194.43978.038CG61.81
13588.29593.8179.215CD182.921
13689.00792.75179.777CE1102.651
13790.17992.31379.159CZ109.251
13890.85291.25679.78OH89.181
13990.61992.93977.96CE299.661
14089.87994.00177.411CD269.911
14186.01996.82677.483C34.971
14285.69197.27376.364O34.191
14386.16997.58278.565N32.381
14486.30499.04378.453CA29.241
14585.13599.76379.121CB26.271
14685.107101.28679.098CG25.211
14784.585101.83777.775CD124.671
14884.28101.78580.275CD224.531
14987.62199.4679.097C29.241
15087.82699.2580.298O29.251
15188.53100.02978.317N28.071
15289.734100.54678.933CA28.031
15390.85999.54178.849CB29.181
15490.136101.86278.332C28.81
15589.368102.44577.575O27.571
15691.322102.33578.721N31.651
15791.939103.5378.17CA33.51
15893.356103.67378.711CB41.291
15993.544104.66679.862CG50.661
16095.033104.97180.112CD60.071
16195.656105.97579.218NE63.451
16296.254105.73678.04CZ64.361
16396.328104.51777.517NH162.131
16496.773106.74677.36NH267.331
16592.007103.36276.675C31.571
16692.51102.34476.197O29.91
16791.483104.33675.933N29.721
16891.441104.19774.485CA28.391
16990.368105.07473.868CB26.881
17090.361104.96272.452OG24.451
17192.772104.54973.881C29.841
17293.417105.53674.279O32.051
17393.179103.74172.91N29.171
17494.362104.03372.111CA29.461
17594.871102.72371.491CB28.251
17695.546102.84670.152CG28.331
17795.134101.70169.258CD28.141
17894.714102.23967.972NE28.971
17994.018101.55567.07CZ31.211
18093.656100.28767.302NH131.641
18193.664102.13965.929NH231.41
18294.068105.15771.07C30.491
18394.991105.67670.432O31.331
18492.785105.53570.939N30.451
18592.3106.53369.955CA28.961
18691.13105.99369.064CB27.21
18791.622104.85468.155CG126.51
18890.578104.29967.207CD126.241
18990.524107.09368.198CG225.991
19091.905107.83970.632C29.661
19192.424108.88870.3O30.371
19290.966107.77671.559N32.081
19390.599108.92772.371CA34.941
19489.658109.86271.607CB35.611
19588.284110.03872.233CG42.511
19688.274111.0773.322CD46.231
19789.316111.6673.609OE153.521
19887.101111.31273.926NE245.861
19989.982108.34173.633C35.651
20089.005107.59173.55O37.81
20190.589108.66674.78N35.491
20290.372107.99576.077CA33.351
20388.996107.4276.284C32.661
20487.985108.0775.964O32.461
20588.963106.20476.829N31.231
20687.749105.3476.852CA30.681
20786.579105.90777.695CB29.611
20886.777106.03379.209CG28.951
20985.434106.14479.895CD128.861
21087.552104.86979.794CD228.651
21187.278104.85975.459C29.571
21286.729105.62774.624O29.331
21387.53103.5775.24N271
21487.195102.87874.015CA24.731
21586.812101.47174.38C23.731
21687.006101.02775.53O23.581
21786.26100.76473.406N23.141
21885.76899.41473.645CA22.661
21984.35499.2773.078CB21.451
22083.54998.23373.85CG20.811
22182.83998.79775.071CD119.691
22282.54997.66472.889CD221.051
22386.71198.473.011C22.291
22486.97298.48871.786O23.251
22587.22797.4673.814N20.041
22688.2396.5173.303CA19.551
22789.43796.46474.221CB20.121
22890.35897.66374.161CG20.931
22991.59197.59673.495CD120.781
23092.45398.68873.461CE121.461
23192.08299.88274.096CZ21.971
23292.905100.99774.077OH22.361
23390.87199.96574.764CE221.971
23490.0298.85974.802CD221.621
23587.69595.10473.134C19.281
23686.72894.74173.775O19.151
23788.31294.29272.29N19.971
23887.8892.89572.203CA21.891
23988.31992.2870.887CB20.491
24088.38392.05873.4C24.021
24189.57392.01873.679O26.521
24287.49591.3974.117N25.381
24387.96890.54175.195CA27.331
24486.98890.5276.344CB27.781
24588.33889.1274.785C29.681
24689.13488.50375.458O35.61
24787.75988.56973.728N31.491
24888.23487.2873.202CA33.841
24987.09686.26573CB38.271
25085.98486.21274.046CG43.831
25184.7885.38873.577CD47.921
25284.03686.01672.474NE58.681
25384.12785.65871.185CZ67.91
25484.92784.65770.815NH174.061
25583.41986.29570.251NH266.641
25688.80287.60771.847C34.131
25788.73988.75471.432O36.321
25889.33186.61971.137N34.511
25989.5686.77169.699CA34.371
26090.38485.669.172CB39.441
26191.84185.64969.592CG42.691
26292.28486.63270.234OD144.681
26392.54884.67669.258OD244.281
26488.20586.69169.032C32.241
26587.35985.93169.476O33.621
26687.98287.44867.968N30.651
26786.6787.42667.3CA30.331
26885.92988.78167.44CB27.291
26985.77789.11968.922CG125.481
27084.76390.1869.214CD124.661
27184.59888.7666.691CG225.681
27286.81687.05165.837C32.291
27387.64187.64265.125O31.971
27486.01386.08665.392N35.31
27586.07885.63264.01CA39.781
27685.30184.34963.84CB47.961
27785.84983.20564.67CG64.331
27885.06381.90964.498CD79.021
27984.73881.55763.342OE191.911
28084.77381.22565.512OE283.791
28185.55786.67963.043C39.771
28284.76187.53463.419O39.611
28386.01986.61361.797N42.631
28485.55587.51860.728CA46.171
28586.16387.12559.362CB47.761
28686.23588.24558.332CG50.191
28786.6787.69756.97CD56.281
28887.02888.78955.946CE55.591
28986.93588.29954.534NZ52.071
29084.03387.46860.667C43.871
29183.43886.43360.989O42.571
29283.4288.58660.284N41.91
29381.96288.68360.124CA41.231
29481.50687.97658.853CB42.371
29582.09988.53957.614CG43.771
29681.66688.17456.36ND145.621
29782.37288.82655.454CE148.911
29883.23189.61556.079NE247.771
29983.07989.45557.432CD245.251
30081.19188.11361.295C39.241
30180.51487.09261.173O40.491
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117184.291110.84872.744OW0991

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SHARPphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.801→38.912 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 898 9.43 %Random selection
Rwork0.1795 8623 --
obs0.1843 9521 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.67 Å2 / Biso mean: 36.0625 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 2.801→38.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 27 52 1269
Biso mean--33.13 32.3 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111253
X-RAY DIFFRACTIONf_angle_d1.0391680
X-RAY DIFFRACTIONf_chiral_restr0.042179
X-RAY DIFFRACTIONf_plane_restr0.004211
X-RAY DIFFRACTIONf_dihedral_angle_d15.75479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8009-2.97640.29481390.206513961535
2.9764-3.20610.25291560.197913831539
3.2061-3.52850.24261400.184914171557
3.5285-4.03860.21661470.158114271574
4.0386-5.08650.19021460.151914571603
5.0865-38.91560.23351700.205515431713

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