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- PDB-2r93: Elongation complex of RNA polymerase II with a hepatitis delta vi... -

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Basic information

Entry
Database: PDB / ID: 2r93
TitleElongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • RNA (5'-R(*UP*GP*AP*UP*UP*CP*UP*CP*UP*AP*UP*CP*GP*GP*AP*AP*UP*C)-3')
KeywordsTransferase/RNA / TRANSFERASE/DNA/RNA / DNA-BINDING / PHOSPHORYLATION / RNA POLYMERASE II / METAL-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION BUBBLE / ELONGATION COMPLEX / TRANSFERASE / TRANSCRIPTION / RNA-DEPENDENT / RNA-DEPENDENT RNA SYNTHESIS / RDRP / DDRP / RNA-BINDING / HEPATITIS DELTA VIRUS / HDV / DNA-directed RNA polymerase / Magnesium / Nucleotidyltransferase / Nucleus / Ubl conjugation / Zinc / Zinc-finger / Polymorphism / Cytoplasm / DNA damage / DNA repair / mRNA processing / Transferase-RNA COMPLEX
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE ...nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / positive regulation of translational initiation / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation from RNA polymerase II promoter / translation initiation factor binding / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 ...Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Enzyme I; Chain A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerase subunit RPB10 / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb5, C-terminal domain / : / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase Rpb3/Rpb11 dimerisation domain / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger, TFIIS-type / C2C2 Zinc finger / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / Gyrase A; domain 2
Similarity search - Domain/homology
RNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 ...RNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsLehmann, E. / Brueckner, F. / Cramer, P.
CitationJournal: Nature / Year: 2007
Title: Molecular basis of RNA-dependent RNA polymerase II activity.
Authors: Lehmann, E. / Brueckner, F. / Cramer, P.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: RNA (5'-R(*UP*GP*AP*UP*UP*CP*UP*CP*UP*AP*UP*CP*GP*GP*AP*AP*UP*C)-3')
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,37722
Polymers519,83013
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)223.336, 394.884, 284.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA (5'-R(*UP*GP*AP*UP*UP*CP*UP*CP*UP*AP*UP*CP*GP*GP*AP*AP*UP*C)-3')


Mass: 5671.372 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in hepatitis delta virus.

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#2: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III largest subunit / B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / DNA-directed RNA polymerase II 140 kDa polypeptide / B150


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa ...RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa polypeptide / B44.5


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P16370, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II 32 kDa polypeptide / B32


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P34087, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P27999, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.6 kDa polypeptide / B13.6


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38902, DNA-directed RNA polymerase

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 kDa polypeptide / ABC27


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20434, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 kDa polypeptide / ABC23


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20435, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 kDa polypeptide / ABC14.4 / ABC14.5


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20436, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 kDa polypeptide / ABC10-beta / ABC8


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22139, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40422, DNA-directed RNA polymerase

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Non-polymers , 2 types, 9 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 6.025 Å3/Da / Density % sol: 79.586 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% (w/v) PEG 6000, 200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes pH 7.0, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2ammonium acetate11
3magnesium acetate11
4Hepes11
5TCEP11
6PEG 600012
7ammonium acetate12
8magnesium acetate12
9Hepes12
10TCEP12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 104533 / Num. obs: 104533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rsym value: 0.149 / Net I/σ(I): 12.4
Reflection shellResolution: 4→4.14 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 10323 / Rsym value: 0.479 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2414 2068 The same set of reflections that has been excluded from previous Pol II structure determinations have been used. Kettenberger et al. Mol. Cell 16, 955-965 (2004)
Rwork0.2165 --
all-102707 -
obs-102707 -
Refinement stepCycle: LAST / Resolution: 4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31202 289 9 0 31500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47344
X-RAY DIFFRACTIONc_bond_d0.008143

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