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- PDB-5zbx: The crystal structure of the nucleosome containing histone H3.1 C... -

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Basic information

Entry
Database: PDB / ID: 5zbx
TitleThe crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D)
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / Nucleosome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein localization to chromosome, centromeric region / CENP-A containing chromatin assembly / condensed chromosome, centromeric region / kinetochore assembly / mitotic cytokinesis / chromosome, centromeric region / mitotic metaphase chromosome alignment / negative regulation of tumor necrosis factor-mediated signaling pathway / pericentric heterochromatin / negative regulation of megakaryocyte differentiation ...protein localization to chromosome, centromeric region / CENP-A containing chromatin assembly / condensed chromosome, centromeric region / kinetochore assembly / mitotic cytokinesis / chromosome, centromeric region / mitotic metaphase chromosome alignment / negative regulation of tumor necrosis factor-mediated signaling pathway / pericentric heterochromatin / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / telomere organization / ChAHP complex assembly / Interleukin-7 signaling / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Resolution of Sister Chromatid Cohesion / Assembly of the ORC complex at the origin of replication / FXIIa activates plasma kallikrein-kinin system / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / NuRD complex assembly / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Interaction of NuRD complexes with transcription factors / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / CHD1 and CHD2 subfamily / establishment of mitotic spindle orientation / HDACs deacetylate histones / CHD6, CHD7, CHD8, CHD9 subfamily / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / epigenetic regulation of gene expression / RHO GTPases Activate Formins / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / kinetochore / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / HCMV Early Events / Metalloprotease DUBs / innate immune response in mucosa / structural constituent of chromatin / Separation of Sister Chromatids / Regulation of PD-L1(CD274) transcription / nucleosome / nucleosome assembly / UCH proteinases / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / killing of cells of another organism / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / Senescence-Associated Secretory Phenotype (SASP) / heterochromatin formation / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain ...Histone, subunit A / Histone, subunit A / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3-like centromeric protein A / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsArimura, Y. / Takagi, H. / Kurumizaka, H.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP17K15043 Japan
Japan Society for the Promotion of ScienceJP25116002 Japan
Japan Society for the Promotion of ScienceJP17H01408 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Agency for Medical Research and DevelopmentBasis for Supporting Innovative Drug Discovery and Life Science Research (BINDS) Japan
CitationJournal: Nat Commun / Year: 2019
Title: The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism.
Authors: Arimura, Y. / Tachiwana, H. / Takagi, H. / Hori, T. / Kimura, H. / Fukagawa, T. / Kurumizaka, H.
History
DepositionFeb 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (146-MER)
J: DNA (146-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,46020
Polymers202,94910
Non-polymers51010
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57170 Å2
ΔGint-471 kcal/mol
Surface area72690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.543, 109.003, 170.136
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 (eV)
11(chain C and resid 15 through 118)
21chain G
12chain A
22(chain E and (resid 38 through 79 or resid 83 through 135))
13chain B
23(chain F and resid 25 through 101)
14(chain D and resid 33 through 124)
24chain H
15chain I
25chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLYSLYS(chain C and resid 15 through 118)CC15 - 11819 - 122
211LYSLYSCLCLchain GGG - M15 - 200119
112PROPROGLUGLUchain AAA38 - 13542 - 139
212PROPROTHRTHR(chain E and (resid 38 through 79 or resid 83 through 135))EE38 - 7942 - 83
222ASPASPGLUGLU(chain E and (resid 38 through 79 or resid 83 through 135))EE83 - 13587 - 139
113ASNASNGLYGLYchain BBB25 - 10129 - 105
213ASNASNGLYGLY(chain F and resid 25 through 101)FF25 - 10129 - 105
114ARGARGALAALA(chain D and resid 33 through 124)DD33 - 12437 - 128
214ARGARGALAALAchain HHH33 - 12437 - 128
115DADAMNMNchain III - P1 - 10031
215DADAMNMNchain JJJ - T147 - 10041

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.1,Histone H3-like centromeric protein A,Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 16078.825 Da / Num. of mol.: 2 / Mutation: V76Q, K77D
Source method: isolated from a genetically manipulated source
Details: Chimera protein H3CATD, in which amino acid residues 76-113 of human histone H3.1 were replaced by the corresponding amino acid residues 75-114 of human CENP-A.
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ, CENPA
Plasmid: pH3.1 CATD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68431, UniProt: P49450
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Plasmid: pH4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: pH2A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06899

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DNA chain , 1 types, 2 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli DH5alpha (bacteria) / Strain (production host): DH5alpha

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Non-polymers , 3 types, 14 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationMonochromator: Rotated-inclined double-crystal monochromator, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→49.276 Å / Num. obs: 59044 / % possible obs: 99.6 % / Redundancy: 13.246 % / Biso Wilson estimate: 62.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.145 / Χ2: 1.191 / Net I/σ(I): 14.72 / Num. measured all: 782121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.58-2.7313.6131.5481.68126398944892850.7071.60998.3
2.73-2.9213.3890.9862.69118772887788710.8521.02599.9
2.92-3.1513.4970.5655.01112039830883010.9540.58799.9
3.15-3.4513.2060.26410.8100858764376370.9920.27599.9
3.45-3.8613.3940.16717.5393114695469520.9950.174100
3.86-4.4513.2260.10625.8281444616261580.9970.1199.9
4.45-5.4413.0840.08531.4568888527452650.9970.08899.8
5.44-7.6412.5170.07334.3251747414141340.9980.07699.8
7.64-49.27611.8280.04648.1828860246524400.9990.04899

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.38 Å49.28 Å
Translation7.38 Å49.28 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CV5

2cv5


Resolution: 2.58→49.276 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2944 5 %
Rwork0.2133 55946 -
obs0.2151 58890 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.4 Å2 / Biso mean: 71.2315 Å2 / Biso min: 27.19 Å2
Refinement stepCycle: final / Resolution: 2.58→49.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6024 5980 10 4 12018
Biso mean--76.2 42.92 -
Num. residues----1047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812820
X-RAY DIFFRACTIONf_angle_d1.02618571
X-RAY DIFFRACTIONf_chiral_restr0.0572109
X-RAY DIFFRACTIONf_plane_restr0.0071336
X-RAY DIFFRACTIONf_dihedral_angle_d25.8046679
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C968X-RAY DIFFRACTION10.745TORSIONAL
12G968X-RAY DIFFRACTION10.745TORSIONAL
21A872X-RAY DIFFRACTION10.745TORSIONAL
22E872X-RAY DIFFRACTION10.745TORSIONAL
31B717X-RAY DIFFRACTION10.745TORSIONAL
32F717X-RAY DIFFRACTION10.745TORSIONAL
41D866X-RAY DIFFRACTION10.745TORSIONAL
42H866X-RAY DIFFRACTION10.745TORSIONAL
51I2912X-RAY DIFFRACTION10.745TORSIONAL
52J2912X-RAY DIFFRACTION10.745TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.58-2.62230.35181390.289526422781100
2.6223-2.66750.29511380.285726202758100
2.6675-2.7160.39971370.286126122749100
2.716-2.76830.33141410.299526652806100
2.7683-2.82480.31971360.289925962732100
2.8248-2.88620.3441400.272126672807100
2.8862-2.95330.30941380.281926292767100
2.9533-3.02720.35691390.306526312770100
3.0272-3.1090.34961390.291126482787100
3.109-3.20050.32961390.262526282767100
3.2005-3.30380.29951400.251626542794100
3.3038-3.42180.30341380.239826352773100
3.4218-3.55880.26331390.225126472786100
3.5588-3.72070.28251400.222726672807100
3.7207-3.91680.24691400.21426562796100
3.9168-4.16210.20871410.193726842825100
4.1621-4.48320.22071410.178626802821100
4.4832-4.9340.2041420.179426892831100
4.934-5.64710.23331420.18627062848100
5.6471-7.11130.22351450.198927412886100
7.1113-49.28490.17651500.16142849299999

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