PDB-8owb: Crystal structure of Mycobacterium smegmatis CoaB in complex with...

ID or keywords:

Entry

Database: PDB / ID: 8owb

Title

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and 2-(5-bromo-1-(4-hydroxyphenyl)-1H-indol-3-yl)-2-oxoacetic acid

Components

Coenzyme A biosynthesis bifunctional protein CoaBC

Keywords

LIGASE / CoaB / CoaBC / Fragment inhibitor

Function / homology

Function and homology information

pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / metal ion binding
Similarity search - Function

Biological species

Mycolicibacterium smegmatis MC2 155 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Mendes, V. / Blundell, T.L.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: Development of new inhibitors against M. tuberculosis CoaBC using a fragment based approach.
Authors: Hess, J. / Mendes, V. / Evans, J.C. / Trapero, A. / Marchetti, C. / Blaszczyk, M. / Bryant, O. / Spry, C. / Coyne, A.G. / Boshoff, H.I.M. / Barry, C.E. / Mizrahi, V. / Blundell, T.L. / Abell, C.

History

Deposition	Apr 27, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8owb.cif.gz	339.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8owb.ent.gz	276.2 KB	Display	PDB format
PDBx/mmJSON format	8owb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/8owb ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8owb	HTTPS FTP

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Related structure data

Related structure data	8ow5C 8owpC 8owqC 8owrC C: citing same article (ref.)
Similar structure data	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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: Coenzyme A biosynthesis bifunctional protein CoaBC

B: Coenzyme A biosynthesis bifunctional protein CoaBC

C: Coenzyme A biosynthesis bifunctional protein CoaBC

D: Coenzyme A biosynthesis bifunctional protein CoaBC

hetero molecules

102 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Coenzyme A biosynthesis bifunctional protein CoaBC

B: Coenzyme A biosynthesis bifunctional protein CoaBC

hetero molecules

defined by author&software
Evidence: gel filtration
51 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Coenzyme A biosynthesis bifunctional protein CoaBC

D: Coenzyme A biosynthesis bifunctional protein CoaBC

hetero molecules

defined by author&software
51 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.877, 76.828, 144.329
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein Mass: 24773.990 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: coaBC, MSMEG_3054 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0QWT2, phosphopantothenoylcysteine decarboxylase, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-VE6 / 2-[5-bromanyl-1-(4-hydroxyphenyl)indol-3-yl]-2-oxidanylidene-ethanoic acid / 2-(5-bromo-1-(4-hydroxyphenyl)-1H-indol-3-yl)-2-oxoacetic acid Mass: 360.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₁₀BrNO₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.05 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% w/v PEG 8000 0.1M MES pH 6.0 0.2M calcium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.25→144.33 Å / Num. obs: 39973 / % possible obs: 98.4 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.114 / R_pim(I) all: 0.048 / R_rim(I) all: 0.124 / Net I/σ(I): 13.1 / Num. measured all: 262162
Reflection shell	Resolution: 2.25→2.39 Å / % possible obs: 98.6 % / Redundancy: 6.5 % / R_merge(I) obs: 0.8 / Num. measured all: 41095 / Num. unique obs: 6348 / CC_1/2: 0.648 / R_pim(I) all: 0.338 / R_rim(I) all: 0.87 / Net I/σ(I) obs: 2.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→72.16 Å / Cross valid method: THROUGHOUT / σ(F): 26.88 / Phase error: 27.93 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2463	1982	4.97 %
R_work	0.2074	-	-
obs	0.2092	39910	98.34 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.25→72.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6250	0	164	325	6739

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6520
X-RAY DIFFRACTION	f_angle_d	1.115	8878
X-RAY DIFFRACTION	f_dihedral_angle_d	14.963	991
X-RAY DIFFRACTION	f_chiral_restr	0.057	1048
X-RAY DIFFRACTION	f_plane_restr	0.016	1163

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 (%)
2.25-2.31	0.3279	148	0.2745	2608	X-RAY DIFFRACTION	92
2.31-2.37	0.3094	165	0.2606	2693	X-RAY DIFFRACTION	94
2.37-2.44	0.2956	152	0.2648	2683	X-RAY DIFFRACTION	95
2.44-2.52	0.3266	141	0.2629	2721	X-RAY DIFFRACTION	95
2.52-2.61	0.2992	127	0.2481	2742	X-RAY DIFFRACTION	96
2.61-2.72	0.2953	139	0.2436	2449	X-RAY DIFFRACTION	85
2.72-2.84	0.2722	107	0.2313	2756	X-RAY DIFFRACTION	96
2.84-2.99	0.2767	123	0.2251	2742	X-RAY DIFFRACTION	96
2.99-3.18	0.3055	117	0.2242	2787	X-RAY DIFFRACTION	96
3.18-3.42	0.2829	133	0.2131	2755	X-RAY DIFFRACTION	95
3.42-3.77	0.2317	129	0.188	2654	X-RAY DIFFRACTION	91
3.77-4.31	0.2368	123	0.176	2663	X-RAY DIFFRACTION	91
4.31-5.43	0.1806	158	0.1662	2811	X-RAY DIFFRACTION	95
5.43-72.16	0.212	177	0.1943	2907	X-RAY DIFFRACTION	94

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	4.6221	-0.7405	0.3298	2.1778	1.0836	3.5828	-0.0689	0.3676	-0.2622	0.0375	0.0543	-0.0735	0.487	-0.1045	-0.0297	0.5515	0.0111	0.002	0.1932	0.0337	0.1813	0.8043	22.3448	-30.8728
2	5.0283	-1.5005	0.7315	5.0738	0.5736	3.2637	0.2142	0.0131	-0.6096	0.1617	-0.085	0.2543	0.6747	-0.2221	-0.089	0.5396	-0.0285	-0.0452	0.2748	0.0317	0.2252	6.5493	17.6077	-28.4592
3	8.7876	-1.7919	-2.004	1.0957	0.7669	2.1615	0.1684	0.5115	0.6199	-0.2862	-0.1101	-0.1225	0.1494	-0.2541	-0.0745	0.4391	-0.0234	-0.0311	0.2078	0.0089	0.1909	4.5243	28.9261	-29.047
4	3.7547	2.0998	-2.6342	4.0057	-3.2143	5.243	-0.0342	0.1613	0.2897	-0.5217	-0.1486	1.8281	-0.2007	-1.4078	0.1709	0.4926	0.0115	-0.1184	0.5862	-0.1316	0.4528	-18.8012	34.4696	-24.077
5	4.2385	0.1231	2.7276	0.0894	0.0938	2.2111	-0.2388	-0.2062	1.8564	-0.0791	-0.0925	-0.1156	-0.2751	-0.1548	0.3746	0.4048	-0.0686	-0.0808	0.2211	0.0108	0.3035	7.4185	35.5113	-25.4342
6	1.8506	-0.3361	1.8236	3.3376	-1.0371	7.0103	0.1899	-0.0327	-0.1427	0.1292	-0.0065	-0.1236	0.6722	-0.0526	-0.2471	0.2883	-0.0213	0.0404	0.2744	0.0132	0.1823	12.9249	32.8083	-34.0083
7	5.3265	-2.7473	3.7481	5.0505	-3.4109	7.7143	-0.2719	-0.2567	0.697	0.4755	-0.0866	0.1893	-0.9392	-0.9156	-0.0972	0.3129	-0.0393	-0.0084	0.2254	0.0212	0.174	11.883	39.3713	-41.017
8	3.3448	-2.493	1.7102	3.1919	-0.7487	8.8499	-0.0015	0.2557	-0.349	-0.6922	0.0484	0.1114	0.0965	-0.3674	-0.2021	0.4878	-0.0131	-0.0132	0.2935	0.0235	0.2517	13.7477	30.0105	-42.529
9	3.9568	-0.315	0.5324	0.1494	0.5258	2.5043	0.376	0.5842	-0.0344	0.2595	0.2737	-0.3478	0.1388	0.7975	-0.5575	0.4914	0.0123	0.0131	0.4155	-0.051	0.2616	16.9626	27.3913	-46.0779
10	5.4781	1.3587	-4.4639	4.8009	0.0615	5.8893	-0.7704	0.9044	-0.0294	-0.9147	0.5586	-0.5798	-0.6396	1.0365	0.2722	0.5264	0.1118	-0.0092	0.4087	0.0128	0.3057	19.1254	20.742	-39.6577
11	4.6226	2.4043	0.5896	2.5681	-0.2155	1.471	0.2724	-0.2936	-0.2271	0.244	-0.099	0.0622	0.2237	-0.0058	-0.1749	0.4103	0.0785	-0.0674	0.3124	-0.023	0.2182	-19.7034	18.3237	-39.3271
12	1.8433	0.5206	0.1755	3.4811	-0.1169	0.392	-0.0197	0.1478	-0.0455	-0.2603	0.0588	0.0352	-0.0041	0.1059	-0.0103	0.4684	0.0878	-0.0346	0.3194	0.0148	0.1883	-22.2759	12.6887	-44.2877
13	3.1359	1.9829	0.2416	4.0198	0.367	0.0854	-0.2041	-0.1369	0.5676	-0.2703	0.0343	0.1781	-0.0526	0.0264	0.0326	0.4452	0.0089	-0.0952	0.3272	-0.0189	0.2766	-19.7348	28.3679	-39.4152
14	8.4003	4.6572	3.575	5.9152	2.053	3.6499	-0.3724	-0.2127	1.2895	0.1682	-0.0821	0.4667	-0.4754	0.1686	0.3428	0.4426	0.0695	-0.0755	0.3538	-0.0432	0.3227	-25.1483	31.9591	-37.1129
15	2.8244	1.3154	-1.2056	6.71	-1.6642	3.9426	-0.1852	-0.5484	-0.087	0.7265	0.432	0.4743	-0.2301	-0.2625	0.2673	0.3705	0.12	0.0125	0.3303	-0.037	0.3162	-35.7891	16.7363	-38.1278
16	4.9119	4.7047	-1.3267	4.5369	-1.3171	5.6291	0.2428	-2.446	1.1406	2.3946	0.0552	1.1806	-0.7629	-0.8126	0.2821	1.1464	0.1775	0.2311	1.2026	-0.2379	0.6253	-37.4917	20.9465	-25.8352
17	4.0857	-0.8304	4.8803	1.1758	-0.2599	6.2846	0.6322	-0.1	-0.2375	0.3002	-0.0217	-0.3976	0.7049	0.5324	-0.5711	0.62	0.0611	-0.053	0.6398	-0.0855	0.4754	-24.976	11.3946	-26.0969
18	0.2358	-1.1217	-0.4548	5.0487	0.7242	4.2081	0.5617	-2.0483	2.0314	0.7634	0.4826	-0.0421	-0.3021	-0.956	-1.331	0.8148	-0.0272	0.1868	0.9357	0.0271	0.7304	-32.002	9.1396	-23.2956
19	4.5223	-2.4358	-1.1041	8.5229	0.192	8.6241	-0.0018	-0.6411	-0.4537	0.307	0.3577	1.0105	0.6277	-0.5936	-0.2167	0.4513	-0.0346	0.0316	0.318	0.0964	0.3439	-33.4742	3.7872	-34.6661
20	4.6	2.936	0.2004	3.6373	3.391	6.0902	0.1453	-0.5753	-0.7301	1.0108	0.3026	-0.9153	1.0761	0.6888	-0.4042	0.5491	-0.0166	-0.0879	0.5721	0.0213	0.2824	2.4002	1.8852	-4.6089
21	1.2556	-1.4186	0.4689	4.405	0.0015	1.3261	0.0174	0.0324	0.113	-0.0892	-0.0301	-0.2905	0.012	0.1794	0.0332	0.2685	-0.0267	0.0365	0.4028	-0.0262	0.2238	-2.0889	15.1836	-6.4278
22	6.6456	3.8572	-0.1743	2.817	-1.8857	5.4563	0.1279	-0.4006	2.0478	-0.1821	-0.2115	1.3213	-1.2199	-0.8632	0.3195	0.5157	-0.0004	-0.0252	0.5432	-0.0964	0.5177	-15.9549	36.8463	-11.3193
23	0.3035	0.7905	0.3	6.1988	-0.8185	2.3433	-0.1386	-0.0425	-0.0668	-0.7201	0.0672	1.2017	-0.1998	-0.3694	-0.0921	0.2665	-0.0654	0.0353	0.3753	-0.0819	0.2542	-16.0004	10.5337	-10.509
24	0.5788	0.518	-0.8182	0.9077	-0.1781	3.594	0.0768	0.1722	-0.1096	-0.0185	0.0656	-0.0093	-0.134	-0.211	-0.0914	0.2892	-0.036	0.0398	0.3324	-0.0097	0.2445	-16.5353	5.8893	0.7541
25	7.8401	-1.1746	-0.6654	5.6732	-4.3258	6.2957	0.1853	-0.6457	-0.4066	0.4992	-0.3527	-0.5302	0.6067	0.7017	0.2151	0.4233	-0.0343	0.0004	0.4708	0.058	0.3125	-6.9534	0.7499	5.8822
26	0.6157	-0.7328	-0.997	1.7024	0.3516	3.5229	-0.2092	0.2614	-0.0189	-0.1696	0.2931	-0.235	0.0275	-0.0721	-0.0599	0.2956	0.1048	-0.0218	0.2496	-0.0266	0.2525	0.2297	38.3344	3.8413
27	7.2155	0.5404	-0.3947	3.1889	-1.7735	2.193	-0.0923	-0.1201	0.0143	0.0554	0.1031	-0.3028	0.1976	-0.0938	-0.0351	0.3928	0.0856	-0.006	0.3258	-0.0432	0.2323	10.895	40.3239	5.9077
28	3.6717	1.1458	0.9803	3.9433	0.9933	3.0258	0.0051	-0.058	0.2296	0.1434	-0.1007	0.4892	0.1479	-0.3506	0.0367	0.3406	0.0488	0.0439	0.3171	-0.0344	0.2771	-8.3559	41.0112	6.0421
29	3.9433	-0.7092	-0.0355	4.3249	-0.3506	4.1006	-0.3258	0.4698	0.4127	-0.7846	0.1769	0.6562	-0.1316	0.2672	-0.2485	0.5678	-0.0438	-0.0182	0.1774	0.0677	0.4928	-1.2097	53.7688	-0.9841
30	6.4361	1.0535	1.4066	3.4882	0.7498	8.587	-0.393	-0.0988	1.566	-1.0158	-0.3955	0.6004	-1.2217	-1.1049	-0.5032	0.6778	0.0448	-0.0796	0.3339	0.1381	0.4304	-1.9018	55.4544	-7.2627
31	1.9674	-1.6409	-2.2286	1.3297	2.0815	4.698	0.7317	-0.6085	0.0856	-1.5648	0.2403	0.366	-0.5328	0.2367	-0.5245	1.3953	-0.0513	-0.1505	0.739	-0.0971	0.5557	7.3786	40.6757	-15.6739
32	5.1759	1.0285	2.3496	3.2583	-3.0391	5.6055	0.958	0.7259	1.1221	-2.3476	-0.3606	0.8647	-0.7993	0.2971	-0.6088	0.9097	-0.0046	0.079	0.4544	0.1391	0.7605	8.1936	54.561	-9.4948
33	3.3923	-4.1383	-3.1511	6.2834	3.5838	7.1862	0.4534	-0.0164	1.0318	-1.3339	-0.0006	0.1419	-1.3993	-0.0014	-0.4397	0.4319	-0.0307	0.0444	0.3595	-0.0104	0.4732	13.2748	53.4318	-0.7953

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 184 through 215 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 216 through 269 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 270 through 284 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 285 through 303 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 304 through 319 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 320 through 342 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 343 through 354 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 355 through 381 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 382 through 393 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 394 through 412 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 184 through 215 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 216 through 269 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 270 through 294 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 295 through 319 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 320 through 342 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 343 through 354 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 355 through 371 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 372 through 393 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 394 through 412 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 185 through 198 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 199 through 284 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 285 through 303 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 304 through 319 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 320 through 354 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 355 through 412 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 184 through 215 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 216 through 247 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 248 through 319 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 320 through 342 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 343 through 361 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 362 through 377 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 378 through 393 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 394 through 412 )

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