BRENDA - Enzyme Database show
show all sequences of 1.3.7.12

Crystal structure of red chlorophyll catabolite reductase: enlargement of the ferredoxin-dependent bilin reductase family

Sugishima, M.; Kitamori, Y.; Noguchi, M.; Kohchi, T.; Fukuyama, K.; J. Mol. Biol. 389, 376-387 (2009)

Data extracted from this reference:

Activating Compound
Activating Compound
Commentary
Organism
Structure
additional information
the catalytic activity of RCCR in vitro dramatically increases by coupling with PaO, possibly due to cooperative action, although PaO has been localized to the plastid envelope and RCCR is a soluble stroma enzyme; the catalytic activity of RCCR in vitro dramatically increases by coupling with pheophorbide alpha oxygenase, which also results in a stereospecific product
Arabidopsis thaliana
Cloned(Commentary)
Commentary
Organism
cloning and expression in Escherichia coli
Arabidopsis thaliana
Crystallization (Commentary)
Crystallization
Organism
at 2.4 A resolution, determination of the crystal structure of, where chloroplast transit peptide is truncated and a Gly-Pro-Leu-Gly-Ser peptide is added to the N terminus, 2 peptide chains A and B are located in an asymmetric unit of the selenomethionine-RCCR crystal, these 2 chains form a homodimer, AtRCCR folds into an alpha/beta/alpha sandwich: 5 N-terminal alpha-helices, an anti-parallel beta-sheet consisting of 8 strands, and 4 C-terminal alpha-helices; purified substrate-free enzyme, with the chloroplast transit peptide truncated and a Gly-Pro-Leu-Gly-Ser peptide added to the N-terminus, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, structure modelling
Arabidopsis thaliana
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
chloroplast
mainly; stroma, constitutive enzyme, the N-terminal 39-amino-acid stretch of RCCR is predicted to be the chloroplast transit peptide
Arabidopsis thaliana
9507
-
mitochondrion
in young seedlings and in response to stress, RCCR is somewhat localized to mitochondria
Arabidopsis thaliana
5739
-
additional information
RCCR is constitutively expressed in chloroplasts, whereas in young seedlings and in response to stress, it is also localized to mitochondria
Arabidopsis thaliana
-
-
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
32000
-
2 * 32000, about, sequence calculation; 2 * 32000, predicted by amino acid sequence, each subunit folds in an alpha/beta/alpha sandwich
Arabidopsis thaliana
60000
-
about, gel filtration; dimer, determined by gel filtration
Arabidopsis thaliana
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
Arabidopsis thaliana
-
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
?
red chlorophyll catabolite + reduced acceptor
Arabidopsis thaliana
the key steps in the degradation pathway of chlorophylls are the ring-opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by RCCR, RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite
primary fluorescent chlorophyll catabolite + oxidized acceptor
in the acidic environment of vacuoles, primary fluorescent chlorophyll catabolite is spontaneously converted into nonfluorescent chlorophyll catabolites
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Arabidopsis thaliana
Q8LDU4
-
-
Purification (Commentary)
Commentary
Organism
anion exchange chromatography
Arabidopsis thaliana
Source Tissue
Source Tissue
Commentary
Organism
Textmining
leaf
-
Arabidopsis thaliana
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
-
699585
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
-
699585
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
formation of a stereospecific product, overview
-
-
?
red chlorophyll catabolite + reduced acceptor
the key steps in the degradation pathway of chlorophylls are the ring-opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by RCCR, RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite
699585
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + oxidized acceptor
in the acidic environment of vacuoles, primary fluorescent chlorophyll catabolite is spontaneously converted into nonfluorescent chlorophyll catabolites
-
-
?
Subunits
Subunits
Commentary
Organism
homodimer
2 * 32000, about, sequence calculation; 2 * 32000, predicted by amino acid sequence, each subunit folds in an alpha/beta/alpha sandwich
Arabidopsis thaliana
More
enzyme RCCR forms a homodimer, in which each subunit folds in an alphabetaalpha sandwich, five N-terminal alpha-helices (H1/H2/H3/H5/H7), an anti-parallel beta-sheet consisting of eight strands (S1-S8), and four C-terminal alpha-helices (H4/H6/H8/H9). The two subunits are related by noncrystallographic 2fold symmetry in which the alpha-helices near the edge of the beta-sheet unique in RCCR participate in intersubunit interaction. The putative RCC-binding site forms an open pocket surrounded by conserved residues among RCCRs. Residues Glu154 and Asp291 stand opposite each other in the substrate binding pocket and are likely involved in substrate binding and/or catalysis. Primary structure comparisons, overview
Arabidopsis thaliana
Cofactor
Cofactor
Commentary
Organism
Structure
Ferredoxin
; dependent on
Arabidopsis thaliana
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
additional information
the catalytic activity of RCCR in vitro dramatically increases by coupling with PaO, possibly due to cooperative action, although PaO has been localized to the plastid envelope and RCCR is a soluble stroma enzyme; the catalytic activity of RCCR in vitro dramatically increases by coupling with pheophorbide alpha oxygenase, which also results in a stereospecific product
Arabidopsis thaliana
Cloned(Commentary) (protein specific)
Commentary
Organism
cloning and expression in Escherichia coli
Arabidopsis thaliana
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
Ferredoxin
; dependent on
Arabidopsis thaliana
Crystallization (Commentary) (protein specific)
Crystallization
Organism
at 2.4 A resolution, determination of the crystal structure of, where chloroplast transit peptide is truncated and a Gly-Pro-Leu-Gly-Ser peptide is added to the N terminus, 2 peptide chains A and B are located in an asymmetric unit of the selenomethionine-RCCR crystal, these 2 chains form a homodimer, AtRCCR folds into an alpha/beta/alpha sandwich: 5 N-terminal alpha-helices, an anti-parallel beta-sheet consisting of 8 strands, and 4 C-terminal alpha-helices; purified substrate-free enzyme, with the chloroplast transit peptide truncated and a Gly-Pro-Leu-Gly-Ser peptide added to the N-terminus, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, structure modelling
Arabidopsis thaliana
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
chloroplast
mainly; stroma, constitutive enzyme, the N-terminal 39-amino-acid stretch of RCCR is predicted to be the chloroplast transit peptide
Arabidopsis thaliana
9507
-
mitochondrion
in young seedlings and in response to stress, RCCR is somewhat localized to mitochondria
Arabidopsis thaliana
5739
-
additional information
RCCR is constitutively expressed in chloroplasts, whereas in young seedlings and in response to stress, it is also localized to mitochondria
Arabidopsis thaliana
-
-
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
32000
-
2 * 32000, about, sequence calculation; 2 * 32000, predicted by amino acid sequence, each subunit folds in an alpha/beta/alpha sandwich
Arabidopsis thaliana
60000
-
about, gel filtration; dimer, determined by gel filtration
Arabidopsis thaliana
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
Arabidopsis thaliana
-
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
?
red chlorophyll catabolite + reduced acceptor
Arabidopsis thaliana
the key steps in the degradation pathway of chlorophylls are the ring-opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by RCCR, RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite
primary fluorescent chlorophyll catabolite + oxidized acceptor
in the acidic environment of vacuoles, primary fluorescent chlorophyll catabolite is spontaneously converted into nonfluorescent chlorophyll catabolites
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
anion exchange chromatography
Arabidopsis thaliana
Source Tissue (protein specific)
Source Tissue
Commentary
Organism
Textmining
leaf
-
Arabidopsis thaliana
-
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
-
699585
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
-
699585
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
formation of a stereospecific product, overview
-
-
?
red chlorophyll catabolite + reduced acceptor
the key steps in the degradation pathway of chlorophylls are the ring-opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by RCCR, RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite
699585
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + oxidized acceptor
in the acidic environment of vacuoles, primary fluorescent chlorophyll catabolite is spontaneously converted into nonfluorescent chlorophyll catabolites
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
2 * 32000, about, sequence calculation; 2 * 32000, predicted by amino acid sequence, each subunit folds in an alpha/beta/alpha sandwich
Arabidopsis thaliana
More
enzyme RCCR forms a homodimer, in which each subunit folds in an alphabetaalpha sandwich, five N-terminal alpha-helices (H1/H2/H3/H5/H7), an anti-parallel beta-sheet consisting of eight strands (S1-S8), and four C-terminal alpha-helices (H4/H6/H8/H9). The two subunits are related by noncrystallographic 2fold symmetry in which the alpha-helices near the edge of the beta-sheet unique in RCCR participate in intersubunit interaction. The putative RCC-binding site forms an open pocket surrounded by conserved residues among RCCRs. Residues Glu154 and Asp291 stand opposite each other in the substrate binding pocket and are likely involved in substrate binding and/or catalysis. Primary structure comparisons, overview
Arabidopsis thaliana
General Information
General Information
Commentary
Organism
evolution
the enzyme belongs to the ferredoxin-dependent bilin reductase (FDBR) family, which synthesizes a variety of phytobilin pigments, on the basis of sequence similarity, ferredoxin dependency, and the common tetrapyrrole skeleton of their substrates. The tertiary structure of RCCR is similar to those of FDBRs, strongly supporting that these enzymes evolved from a common ancestor
Arabidopsis thaliana
additional information
Residues Glu154 and Asp291 stand opposite each other in the substrate binding pocket and are likely involved in substrate binding and/or catalysis
Arabidopsis thaliana
physiological function
the key steps in the degradation pathway of chlorophylls are the ring opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by red chlorophyll catabolite reductase (RCCR). During these steps, chlorophyll catabolites lose their color and phototoxicity. Enzyme RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite
Arabidopsis thaliana
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme belongs to the ferredoxin-dependent bilin reductase (FDBR) family, which synthesizes a variety of phytobilin pigments, on the basis of sequence similarity, ferredoxin dependency, and the common tetrapyrrole skeleton of their substrates. The tertiary structure of RCCR is similar to those of FDBRs, strongly supporting that these enzymes evolved from a common ancestor
Arabidopsis thaliana
additional information
Residues Glu154 and Asp291 stand opposite each other in the substrate binding pocket and are likely involved in substrate binding and/or catalysis
Arabidopsis thaliana
physiological function
the key steps in the degradation pathway of chlorophylls are the ring opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by red chlorophyll catabolite reductase (RCCR). During these steps, chlorophyll catabolites lose their color and phototoxicity. Enzyme RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite
Arabidopsis thaliana
Other publictions for EC 1.3.7.12
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
736190
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726877
Sakuraba
7-Hydroxymethyl chlorophyll a ...
Arabidopsis thaliana
Biochem. Biophys. Res. Commun.
430
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2013
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726165
Sakuraba
STAY-GREEN and chlorophyll cat ...
Arabidopsis thaliana
Plant Cell
24
507-518
2012
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736688
Zhang
Correlation of leaf senescence ...
Brassica rapa
J. Plant Physiol.
168
2081-2087
2011
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712769
Sugishima
Crystal structures of the subs ...
Arabidopsis thaliana
J. Mol. Biol.
402
879-891
2010
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699585
Sugishima
Crystal structure of red chlor ...
Arabidopsis thaliana
J. Mol. Biol.
389
376-387
2009
1
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700695
Ougham
The control of chlorophyll cat ...
Arabidopsis thaliana
Plant Biol.
10 Suppl 1
4-14
2008
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676436
Pruzinska
In vivo participation of red c ...
Arabidopsis thaliana
Plant Cell
19
369-387
2007
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671354
Hörtensteiner
Chlorophyll degradation during ...
Arabidopsis sp., Hordeum vulgare, Solanum lycopersicum, Spinacia oleracea
Annu. Rev. Plant Biol.
57
55-77
2006
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735438
Hoertensteiner
Chlorophyll degradation during ...
Arabidopsis thaliana
Annu. Plant Biol.
57
55-77
2006
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676587
Pruzinska
Chlorophyll breakdown in senes ...
Arabidopsis thaliana
Plant Physiol.
139
52-63
2005
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736960
Roca
Analysis of the chlorophyll ca ...
Lolium temulentum
Phytochemistry
65
1231-1238
2004
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676913
Mach
The Arabidopsis-accelerated ce ...
Arabidopsis sp.
Proc. Natl. Acad. Sci. USA
98
771-776
2001
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676395
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18
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-
38
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1
-
-
-
1
-
-
15
-
-
-
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-
-
15
-
2
-
-
3
-
-
27
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-
15
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-
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-
-
18
-
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38
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1
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1
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15
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2
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3
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2
1
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1
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2
1
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1
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1
-
2
2
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-
1
2
-
3
-
-
2
1
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-
-
-
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-
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2
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2
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2
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3
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1
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2
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2
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1
2
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2
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2
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3
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1
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4
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4
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2
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2
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1
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4
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2
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2
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4
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4
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4
4
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735913
Hoertensteiner
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5
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16
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7
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7
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5
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6
14
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9
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5
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1
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5
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16
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1
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1
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2
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1
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1
1
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1
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1
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2
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