PDB-3rrh: Ternary Structure of the large fragment of Taq DNA polymerase bou...

ID or keywords:

Entry

Database: PDB / ID: 3rrh

Title

Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddTTP

Components

(5'-D(*AP*AP*AP*(3DR)P*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3')
DNA polymerase I, thermostable

Keywords

TRANSFERASE/DNA / DNA polymerase / Abasic site / Translesion synthesis / A-rule / TRANSFERASE-DNA complex

Function / homology

Function and homology information

nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding
Similarity search - Function

Biological species

Thermus aquaticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Marx, A. / Diederichs, K. / Obeid, S.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Authors: Obeid, S. / Welte, W. / Diederichs, K. / Marx, A.

History

Deposition	Apr 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2012	Group: Database references
Revision 1.2	May 9, 2012	Group: Database references
Revision 1.3	Sep 13, 2023	Group: 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_site 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rrh.cif.gz	265.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3rrh.ent.gz	208 KB	Display	PDB format
PDBx/mmJSON format	3rrh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rrh_validation.pdf.gz	800.7 KB	Display	wwPDB validaton report
Full document	3rrh_full_validation.pdf.gz	806.5 KB	Display
Data in XML	3rrh_validation.xml.gz	26.7 KB	Display
Data in CIF	3rrh_validation.cif.gz	38.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rr/3rrh ftp://data.pdbj.org/pub/pdb/validation_reports/rr/3rrh	HTTPS FTP

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Related structure data

Related structure data	3rr7C 3rr8C 3rrgC 3t3fC 3lwlS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3rrg-d 3rr8-d 4c8k-d 3po4-d 3m8s-d 4df4-d 1qtm-d 3syz-d 4dfm-d 4elv-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #3 - Mar 2000 DNA Polymerase similarity (24) #91 - Jul 2007 Thymine Dimers similarity (7) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (3) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #150 - Jun 2012 Sliding Clamps similarity (5) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #55 - Jul 2004 DNA Ligase similarity (3) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #121 - Jan 2010 70S Ribosomes similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
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TAL Effectors
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similarity (1)
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similarity (1)
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similarity (1)
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Deposited unit

A: DNA polymerase I, thermostable

B: (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3')

C: (5'-D(*AP*AP*AP*(3DR)P*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')

hetero molecules

70.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	108.305, 108.305, 90.151
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-895- HOH
2	1	A-899- HOH
3	1	A-901- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	DNA polymerase I, thermostable / Taq polymerase 1 Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: klenow fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

#1: Protein

DNA polymerase I, thermostable / Taq polymerase 1

Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: klenow fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Plasmid: pET-21b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain	(5'-D(GPAPCPCPAPCPGPGPCPGPCP(2DT))-3') Mass: 3632.382 Da / Num. of mol.: 1 / Fragment: DNA primer / Source method: obtained synthetically
#3: DNA chain	(5'-D(APAPAP(3DR)PAPGPCPGPCPCPGPTPGPGPTPC)-3') Mass: 4799.107 Da / Num. of mol.: 1 / Fragment: DNA template / Source method: obtained synthetically

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Non-polymers , 6 types, 372 molecules

#4: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2010
Radiation	Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 574388 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.95 % / R_merge(I) obs: 0.097 / Net I/σ(I): 15.23
Reflection shell	Resolution: 1.79→1.9 Å / Redundancy: 9.82 % / R_merge(I) obs: 1.2 / Mean I/σ(I) obs: 2.12 / Num. unique all: 88487 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHENIX	(phenix.refine: dev_613)	model building
PHENIX	(phenix.refine: dev_613)	refinement
PHENIX	dev_613	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LWL

3lwl

Resolution: 1.8→46.897 Å / SU ML: 0.23 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 19.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2006	5563	5.07 %	random
R_work	0.1664	-	-	-
obs	0.1681	56845	99.99 %	-
all	-	109630	-	-

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.725 Å² / k_sol: 0.354 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.7964 Å²	0 Å²	0 Å²
2-	-	9.7964 Å²	0 Å²
3-	-	-	6.6355 Å²

Refine analyze

Luzzati coordinate error obs: 0.23 Å

Refinement step

Cycle: LAST / Resolution: 1.8→46.897 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4261	520	69	362	5212

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5042
X-RAY DIFFRACTION	f_angle_d	1.003	6936
X-RAY DIFFRACTION	f_dihedral_angle_d	15.54	1952
X-RAY DIFFRACTION	f_chiral_restr	0.062	755
X-RAY DIFFRACTION	f_plane_restr	0.004	809

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.8205	0.2927	174	0.261	3485	X-RAY DIFFRACTION	100
1.8205-1.8419	0.3273	222	0.2565	3433	X-RAY DIFFRACTION	100
1.8419-1.8643	0.2511	185	0.2459	3449	X-RAY DIFFRACTION	100
1.8643-1.8879	0.2717	171	0.2222	3451	X-RAY DIFFRACTION	100
1.8879-1.9128	0.2801	199	0.2279	3518	X-RAY DIFFRACTION	100
1.9128-1.939	0.2656	166	0.2128	3449	X-RAY DIFFRACTION	100
1.939-1.9667	0.2495	206	0.1949	3461	X-RAY DIFFRACTION	100
1.9667-1.996	0.2257	207	0.1914	3393	X-RAY DIFFRACTION	100
1.996-2.0272	0.2321	188	0.1923	3469	X-RAY DIFFRACTION	100
2.0272-2.0605	0.2365	177	0.1954	3494	X-RAY DIFFRACTION	100
2.0605-2.096	0.2109	177	0.1879	3490	X-RAY DIFFRACTION	100
2.096-2.1341	0.2143	167	0.1686	3502	X-RAY DIFFRACTION	100
2.1341-2.1752	0.1982	172	0.1643	3490	X-RAY DIFFRACTION	100
2.1752-2.2196	0.2142	151	0.1636	3452	X-RAY DIFFRACTION	100
2.2196-2.2678	0.2292	187	0.1583	3506	X-RAY DIFFRACTION	100
2.2678-2.3206	0.2241	168	0.1645	3464	X-RAY DIFFRACTION	100
2.3206-2.3786	0.234	167	0.1703	3458	X-RAY DIFFRACTION	100
2.3786-2.4429	0.2514	161	0.1747	3535	X-RAY DIFFRACTION	100
2.4429-2.5148	0.2035	211	0.171	3491	X-RAY DIFFRACTION	100
2.5148-2.596	0.2171	180	0.1722	3433	X-RAY DIFFRACTION	100
2.596-2.6887	0.2481	190	0.1767	3458	X-RAY DIFFRACTION	100
2.6887-2.7964	0.2341	196	0.1736	3478	X-RAY DIFFRACTION	100
2.7964-2.9236	0.1895	191	0.1692	3486	X-RAY DIFFRACTION	100
2.9236-3.0777	0.2039	161	0.1731	3462	X-RAY DIFFRACTION	100
3.0777-3.2705	0.188	209	0.165	3461	X-RAY DIFFRACTION	100
3.2705-3.523	0.162	179	0.1452	3478	X-RAY DIFFRACTION	100
3.523-3.8773	0.1685	225	0.1467	3428	X-RAY DIFFRACTION	100
3.8773-4.438	0.1833	200	0.1406	3446	X-RAY DIFFRACTION	100
4.438-5.59	0.1686	175	0.1499	3480	X-RAY DIFFRACTION	100
5.59-46.9133	0.1702	201	0.1568	3467	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.1038	0.0338	0.0546	0.0176	0.0149	0.3324	-0.0057	0.0524	-0.2202	-0.1705	-0.0234	-0.328	0.2381	0.0486	0.0456	0.1519	0.0073	0.0814	0.0455	0.0024	0.2474	42.4524	-42.7614	-17.7714
2	0.162	0.0057	-0.081	0.1258	-0.1073	0.13	0.0451	-0.056	0.01	0.1313	-0.0862	0.0711	-0.017	-0.0163	-0.0161	0.0863	-0.1386	0.0583	-0.0225	-0.026	0.0912	34.1803	-15.5813	-2.2456
3	0.0313	-0.035	-0.0661	0.1222	0.11	0.179	-0.014	-0.0315	0.0513	-0.0182	0.031	0.0681	-0.1043	-0.1536	0.0063	0.0396	0.0093	-0.0002	0.2007	0.0468	0.0912	13.6542	-17.8888	-17.884
4	0.0607	-0.032	-0.0437	0.2463	0.0609	0.0372	-0.0043	-0.1036	0.0381	0.1531	0.0431	0.0384	-0.089	-0.0281	-0.024	0.2416	0.1547	0.0028	0.2735	-0.0253	0.1313	7.067	-12.1801	-0.8209
5	0.0121	0.0008	-0.004	0.0021	-0.0015	0.0083	-0.0102	-0.0768	-0.0571	0.0116	0.0223	0.0568	0.0291	-0.148	-0.0341	0.0302	-0.0965	0.0052	0.2169	0.0592	0.09	9.2124	-34.5608	-5.3527
6	0.1375	0.0653	-0.0675	0.2174	-0.0673	0.1444	-0.0667	-0.0447	-0.085	-0.083	0.0365	0.0376	0.0497	-0.0266	0.0241	0.0644	-0.036	0.0329	0.1357	0.0257	0.0393	21.6332	-27.9569	-12.2977
7	0.129	-0.168	-0.1746	0.23	0.2465	0.2753	-0.0039	0.1128	0.0848	-0.1071	0.0901	0.0292	-0.1947	-0.1849	-0.0506	0.1242	-0.012	-0.0096	0.1352	0.0357	0.0578	23.1276	-15.0844	-25.6575
8	-0.0002	0.003	0.0007	0.0138	0.0064	0.014	0.0106	-0.0067	-0.0631	0.0314	-0.0277	-0.0468	-0.0441	0.0866	0.0001	0.0716	-0.0062	0.006	0.1	0.0118	0.1175	36.5302	-22.836	4.0055
9	0.0483	0.0163	-0.0276	0.0101	0.015	0.1208	-0.1296	-0.0293	-0.0614	0.0595	0.027	-0.0474	0.0497	0.0201	-0.0273	0.0482	0.0136	-0.0207	0.0846	0.0107	0.0683	35.0887	-24.0452	5.8257

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 295:418)
2	X-RAY DIFFRACTION	2	(chain A and resid 419:600)
3	X-RAY DIFFRACTION	3	(chain A and resid 601:637)
4	X-RAY DIFFRACTION	4	(chain A and resid 638:696)
5	X-RAY DIFFRACTION	5	(chain A and resid 697:731)
6	X-RAY DIFFRACTION	6	(chain A and resid 732:786)
7	X-RAY DIFFRACTION	7	(chain A and resid 787:832)
8	X-RAY DIFFRACTION	8	(chain B)
9	X-RAY DIFFRACTION	9	(chain C)

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Protein , 1 types, 1 molecules A

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DNA chain , 2 types, 2 molecules BC

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Non-polymers , 6 types, 372 molecules

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Experiment

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Protein , 1 types, 1 molecules A

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DNA chain , 2 types, 2 molecules BC

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Non-polymers , 6 types, 372 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi