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- PDB-3ubt: Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3ubt
TitleCrystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA
Components
  • 5'-D(*TP*GP*GP*CP*CP*A)-3'
  • Modification methylase HaeIII
KeywordsTRANSFERASE/DNA / Protein-DNA complex / DNA cytosine-5 methyltransferase / DNA binding / S-Adenosyl methionine binding / Cytosine-5 DNA methylation / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / DNA restriction-modification system / negative regulation of gene expression via chromosomal CpG island methylation / methylation / DNA binding / ATP binding
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / Type II methyltransferase M.HaeIII
Similarity search - Component
Biological speciesHaemophilus aegyptius (Koch-Weeks bacillus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsVerdine, G.L. / Didovyk, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural origins of DNA target selection and nucleobase extrusion by a DNA Cytosine methyltransferase.
Authors: Didovyk, A. / Verdine, G.L.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Oct 8, 2014Group: Refinement description
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Modification methylase HaeIII
A: Modification methylase HaeIII
B: Modification methylase HaeIII
D: 5'-D(*TP*GP*GP*CP*CP*A)-3'
E: 5'-D(*TP*GP*GP*CP*CP*A)-3'
F: 5'-D(*TP*GP*GP*CP*CP*A)-3'
G: 5'-D(*TP*GP*GP*CP*CP*A)-3'
H: 5'-D(*TP*GP*GP*CP*CP*A)-3'
C: 5'-D(*TP*GP*GP*CP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,23918
Polymers124,3679
Non-polymers2,8719
Water10,233568
1
Y: Modification methylase HaeIII
G: 5'-D(*TP*GP*GP*CP*CP*A)-3'
H: 5'-D(*TP*GP*GP*CP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9207
Polymers41,4563
Non-polymers1,4644
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-21 kcal/mol
Surface area16480 Å2
MethodPISA
2
A: Modification methylase HaeIII
E: 5'-D(*TP*GP*GP*CP*CP*A)-3'
F: 5'-D(*TP*GP*GP*CP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4136
Polymers41,4563
Non-polymers9573
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-23 kcal/mol
Surface area16340 Å2
MethodPISA
3
B: Modification methylase HaeIII
D: 5'-D(*TP*GP*GP*CP*CP*A)-3'
C: 5'-D(*TP*GP*GP*CP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9065
Polymers41,4563
Non-polymers4502
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-17 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.564, 129.588, 132.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31Y
12A
22B
32Y
13A
23B
33Y
14A
24B
34Y
15A
25B
35Y
16A
26B
36Y
17A
27B
37Y
18A
28B
38Y
19A
29B
39Y
110A
210B
310Y
111A
211B
311Y
112A
212B
312Y
113A
213B
313Y
114A
214B
314Y

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and resid 191:197)
211(chain B and resid 191:197)
311(chain Y and resid 191:197)
112(chain A and resid 212:219) and not (resid 216)
212(chain B and resid 212:219) and not (resid 216)
312(chain Y and resid 212:219) and not (resid 216)
113(chain A and resid 223:238) and not (resid 225 or resid 229)
213(chain B and resid 223:238) and not (resid 225 or resid 229)
313(chain Y and resid 223:238) and not (resid 225 or resid 229)
114(chain A and resid 245:250) and not (resid 248)
214(chain B and resid 245:250) and not (resid 248)
314(chain Y and resid 245:250) and not (resid 248)
115(chain A and resid 276:305) and not (resid 289 or resid 291 or resid 293 or resid 295 or resid 299)
215(chain B and resid 276:305) and not (resid 289 or resid 291 or resid 293 or resid 295 or resid 299)
315(chain Y and resid 276:305) and not (resid 289 or resid 291 or resid 293 or resid 295 or resid 299)
116(chain A and (resid 2:5))
216(chain B and (resid 2:5))
316(chain Y and (resid 2:5))
117(chain A and (resid 15:17))
217(chain B and (resid 15:17))
317(chain Y and (resid 15:17))
118(chain A and (resid 22:47)) and not (resid 30 or resid 35:36)
218(chain B and (resid 22:47)) and not (resid 30 or resid 35:36)
318(chain Y and (resid 22:47)) and not (resid 30 or resid 35:36)
119(chain A and (resid 59:68)) and not (resid 61)
219(chain B and (resid 59:68)) and not (resid 61)
319(chain Y and (resid 59:68)) and not (resid 61)
1110(chain A and (resid 71:82)) and not (resid 72 or resid 75:76)
2110(chain B and (resid 71:82)) and not (resid 72 or resid 75:76)
3110(chain Y and (resid 71:82)) and not (resid 72 or resid 75:76)
1111(chain A and (resid 99:110)) and not (resid 100 or resid 102 resid 105)
2111(chain B and (resid 99:110)) and not (resid 100 or resid 102 resid 105)
3111(chain Y and (resid 99:110)) and not (resid 100 or resid 102 resid 105)
1112(chain A and (resid 122:162)) and not (resid 132 or...
2112(chain B and (resid 122:162)) and not (resid 132 or...
3112(chain Y and (resid 122:162)) and not (resid 132 or...
1113(chain A and (resid 167:169))
2113(chain B and (resid 167:169))
3113(chain Y and (resid 167:169))
1114(chain A and (resid 308:324)) and not (resid 311 or...
2114(chain B and (resid 308:324)) and not (resid 311 or...
3114(chain Y and (resid 308:324)) and not (resid 311 or...

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(-0.999076, -0.03587, -0.023674), (-0.033066, 0.99341, -0.109746), (0.027455, -0.108862, -0.993678)-1.62613, -27.811199, -68.1493
2given(0.999467, -0.029305, 0.014411), (0.028731, 0.998844, 0.038532), (-0.015523, -0.038097, 0.999153)0.810595, -42.594002, 0.843774
3given(-0.999126, -0.02439, -0.033958), (-0.021932, 0.997237, -0.070975), (0.035595, -0.070169, -0.9969)-2.00544, -26.655701, -68.2342
4given(0.999679, -0.02223, 0.01213), (0.02158, 0.998449, 0.051324), (-0.013252, -0.051045, 0.998608)0.583679, -42.334, 1.16304
5given(-0.999107, -0.023035, -0.035415), (-0.02009, 0.996481, -0.081371), (0.037165, -0.080587, -0.996054)-2.01904, -27.0418, -68.2603
6given(0.999936, -0.010647, 0.003929), (0.010492, 0.999243, 0.037467), (-0.004325, -0.037424, 0.99929)0.191265, -43.002499, 1.11685
7given(-0.998334, -0.030991, -0.048673), (-0.026558, 0.995658, -0.089218), (0.051227, -0.087777, -0.994822)-2.53546, -27.273001, -68.5168
8given(0.99994, -0.010158, 0.004025), (0.010025, 0.999449, 0.031654), (-0.004344, -0.031612, 0.999491)0.247526, -43.162601, 1.14574
9given(-0.998988, -0.026978, -0.036), (-0.023544, 0.995423, -0.09262), (0.038334, -0.091679, -0.995051)-2.0851, -27.402399, -68.348396
10given(0.999816, -0.017507, 0.007892), (0.017181, 0.999064, 0.039701), (-0.00858, -0.039558, 0.99918)0.320338, -42.7705, 1.04512
11given(-0.99974, -0.020464, -0.01004), (-0.019638, 0.996877, -0.076491), (0.011574, -0.076274, -0.99702)-0.760136, -26.6164, -67.851303
12given(0.999413, -0.024522, -0.023926), (0.025566, 0.998688, 0.044373), (0.022806, -0.044958, 0.998728)0.200296, -42.973701, 1.51075
13given(-0.999499, 0.00157, -0.031597), (0.00358, 0.997964, -0.063685), (0.031432, -0.063766, -0.99747)-1.72553, -26.0956, -67.8974
14given(0.999983, 0.000161, 0.005772), (-0.000331, 0.999564, 0.029518), (-0.005765, -0.02952, 0.999548)0.118616, -43.255901, 1.02006
15given(-0.999903, -0.009726, -0.010015), (-0.008941, 0.997092, -0.07568), (0.010722, -0.075583, -0.997082)-0.62485, -26.7115, -67.882202
16given(0.999915, -0.008122, -0.010163), (0.008384, 0.999627, 0.025975), (0.009948, -0.026058, 0.999611)0.018573, -43.134998, 1.19482
17given(-0.999778, -0.014325, -0.015431), (-0.013273, 0.997716, -0.066224), (0.016344, -0.066005, -0.997685)-1.03355, -25.986, -67.865097
18given(0.99993, -0.010532, -0.005396), (0.010636, 0.99975, 0.019674), (0.005187, -0.01973, 0.999792)0.019979, -43.115898, 1.11366
19given(-0.999837, -0.016295, 0.007744), (-0.017005, 0.994559, -0.102777), (-0.006027, -0.102892, -0.994674)0.2523, -28.317499, -68.289803
20given(0.999995, 0.002881, -0.001305), (-0.002853, 0.999778, 0.020873), (0.001365, -0.020869, 0.999781)0.106555, -43.136902, 1.26911
21given(-0.999864, -0.014526, -0.007833), (-0.013407, 0.991715, -0.127754), (0.009624, -0.127632, -0.991775)-0.568643, -30.5602, -68.285301
22given(0.992138, 0.09806, -0.077758), (-0.096496, 0.995053, 0.023634), (0.079691, -0.015945, 0.996692)-0.359926, -42.759399, 0.995422
23given(-0.999862, -0.016322, -0.003134), (-0.016041, 0.997066, -0.074843), (0.004346, -0.074783, -0.99719)-0.403817, -26.663401, -67.688301
24given(0.999888, -0.014354, -0.004284), (0.014468, 0.999503, 0.028021), (0.003879, -0.028079, 0.999598)0.034673, -43.1064, 1.23502
25given(-0.999815, 0.001235, -0.01918), (0.002606, 0.997428, -0.071634), (0.019042, -0.07167, -0.997247)-0.891412, -26.5375, -67.532204
26given(0.999956, 0.006363, 0.006889), (-0.006564, 0.999539, 0.029652), (-0.006698, -0.029696, 0.999537)0.286316, -43.232399, 1.14268
27given(-0.999999, 0.001355, -3.46028), (0.001353, 0.99722, -0.074495), (-6.64047, -0.029696, 0.999537)0.273323, -26.7609, -67.585602
28given(0.999923, -0.00683, -0.010402), (0.007074, 0.999696, 0.023636), (0.010238, -0.023708, 0.999667)0.026667, -43.185398, 1.23792

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Components

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Protein / DNA chain , 2 types, 9 molecules YABDEFGHC

#1: Protein Modification methylase HaeIII / M.HaeIII / Cytosine-specific methyltransferase HaeIII


Mass: 37837.344 Da / Num. of mol.: 3 / Mutation: C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus aegyptius (Koch-Weeks bacillus)
Gene: haeIIIM / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): LC1061
References: UniProt: P20589, DNA (cytosine-5-)-methyltransferase
#2: DNA chain
5'-D(*TP*GP*GP*CP*CP*A)-3'


Mass: 1809.218 Da / Num. of mol.: 6 / Source method: obtained synthetically

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Non-polymers , 4 types, 577 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 6

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26-27% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100 mM ammonium sulfate, 50 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorDate: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→17 Å / Num. all: 35072 / Num. obs: 31721 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 30.733 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.5-2.62.460.373.4193443805267970.4
2.6-2.693.520.3364.18104932983276292.6
2.69-2.813.520.2724.98119243386316893.6
2.81-2.963.540.2075.98124893525330593.8
2.96-3.153.550.1776.89127143583333993.2
3.15-3.393.520.1388.34121403447323994
3.39-3.733.510.1089.95122463486328094.1
3.73-4.263.450.09211.13120093481327494.1
4.26-5.343.380.08311.74120083550332993.8
5.34-173.190.06811.05122063826334687.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→16.981 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.31 / Isotropic thermal model: Isotropic / σ(F): 2.01 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1533 4.84 %RANDOM
Rwork0.1822 ---
obs0.1841 31673 90.93 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.008 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 118.94 Å2 / Biso mean: 22.2128 Å2 / Biso min: 3.52 Å2
Baniso -1Baniso -2Baniso -3
1--4.4419 Å20 Å20 Å2
2--3.8727 Å2-0 Å2
3---0.5691 Å2
Refinement stepCycle: LAST / Resolution: 2.502→16.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7835 711 122 568 9236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028959
X-RAY DIFFRACTIONf_angle_d0.64212255
X-RAY DIFFRACTIONf_chiral_restr0.0441292
X-RAY DIFFRACTIONf_plane_restr0.0021456
X-RAY DIFFRACTIONf_dihedral_angle_d14.2523388
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A48X-RAY DIFFRACTIONPOSITIONAL0.008
12B48X-RAY DIFFRACTIONPOSITIONAL0.008
13Y51X-RAY DIFFRACTIONPOSITIONAL0.008
21A64X-RAY DIFFRACTIONPOSITIONAL0.009
22B64X-RAY DIFFRACTIONPOSITIONAL0.009
23Y64X-RAY DIFFRACTIONPOSITIONAL0.007
31A117X-RAY DIFFRACTIONPOSITIONAL0.007
32B117X-RAY DIFFRACTIONPOSITIONAL0.007
33Y117X-RAY DIFFRACTIONPOSITIONAL0.006
41A39X-RAY DIFFRACTIONPOSITIONAL0.007
42B39X-RAY DIFFRACTIONPOSITIONAL0.007
43Y39X-RAY DIFFRACTIONPOSITIONAL0.006
51A203X-RAY DIFFRACTIONPOSITIONAL0.008
52B203X-RAY DIFFRACTIONPOSITIONAL0.008
53Y203X-RAY DIFFRACTIONPOSITIONAL0.007
61A30X-RAY DIFFRACTIONPOSITIONAL0.006
62B30X-RAY DIFFRACTIONPOSITIONAL0.006
63Y30X-RAY DIFFRACTIONPOSITIONAL0.009
71A23X-RAY DIFFRACTIONPOSITIONAL0.009
72B23X-RAY DIFFRACTIONPOSITIONAL0.009
73Y23X-RAY DIFFRACTIONPOSITIONAL0.006
81A185X-RAY DIFFRACTIONPOSITIONAL0.008
82B185X-RAY DIFFRACTIONPOSITIONAL0.008
83Y183X-RAY DIFFRACTIONPOSITIONAL0.006
91A60X-RAY DIFFRACTIONPOSITIONAL0.006
92B60X-RAY DIFFRACTIONPOSITIONAL0.006
93Y60X-RAY DIFFRACTIONPOSITIONAL0.006
101A63X-RAY DIFFRACTIONPOSITIONAL0.008
102B63X-RAY DIFFRACTIONPOSITIONAL0.008
103Y63X-RAY DIFFRACTIONPOSITIONAL0.007
111A9X-RAY DIFFRACTIONPOSITIONAL0.007
112B9X-RAY DIFFRACTIONPOSITIONAL0.007
113Y9X-RAY DIFFRACTIONPOSITIONAL0.017
121A285X-RAY DIFFRACTIONPOSITIONAL0.007
122B285X-RAY DIFFRACTIONPOSITIONAL0.007
123Y285X-RAY DIFFRACTIONPOSITIONAL0.007
131A28X-RAY DIFFRACTIONPOSITIONAL0.006
132B28X-RAY DIFFRACTIONPOSITIONAL0.006
133Y28X-RAY DIFFRACTIONPOSITIONAL0.007
141A102X-RAY DIFFRACTIONPOSITIONAL0.009
142B102X-RAY DIFFRACTIONPOSITIONAL0.009
143Y102X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5024-2.58290.29671190.24511988210768
2.5829-2.67480.32831380.23762743288193
2.6748-2.78150.2841080.22642808291693
2.7815-2.90750.27221430.1972793293694
2.9075-3.05990.21681270.1972780290793
3.0599-3.25040.241490.1882805295493
3.2504-3.49930.2181590.18052795295494
3.4993-3.84780.19091590.15652852301195
3.8478-4.39610.15751540.14422830298494
4.3961-5.50710.1721510.14962854300594
5.5071-16.98170.28081260.2012892301890

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