PDB-8ow5: Crystal structure of Mycobacterium smegmatis CoaB in complex with...

ID or keywords:

Entry

Database: PDB / ID: 8ow5

Title

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and 5-methoxy-1H-indole-2-carboxylic 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 complex /

phosphopantothenoylcysteine decarboxylase /

phosphopantothenoylcysteine decarboxylase activity / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase 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: 2.84 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	8ow5.cif.gz	322.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8ow5.ent.gz	263.7 KB	Display	PDB format
PDBx/mmJSON format	8ow5.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/8ow5 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8ow5	HTTPS FTP

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Related structure data

Related structure data	8owbC 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

101 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
50.8 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
50.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.734, 77.478, 144.804
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 / Cytidine 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-VEO / 5-methoxy-1H-indole-2-carboxylic acid Mass: 191.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₉NO₃ / Feature type: SUBJECT OF INVESTIGATION
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: 2.17 Å³/Da / Density % sol: 43.37 %
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: I04-1 / Wavelength: 0.92819 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92819 Å / Relative weight: 1
Reflection	Resolution: 2.84→77.48 Å / Num. obs: 21062 / % possible obs: 100 % / Redundancy: 7.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.039 / R_rim(I) all: 0.11 / Net I/σ(I): 15.9 / Num. measured all: 167266
Reflection shell	Resolution: 2.84→2.99 Å / % possible obs: 100 % / Redundancy: 8.2 % / R_merge(I) obs: 0.82 / Num. measured all: 24631 / Num. unique obs: 3019 / CC_1/2: 0.79 / R_pim(I) all: 0.305 / R_rim(I) all: 0.876 / Net I/σ(I) obs: 2.4

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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: 2.84→68.31 Å / Cross valid method: THROUGHOUT / σ(F): 39.39 / Phase error: 33.47 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2952	1041	4.95 %
R_work	0.2182	-	-
obs	0.2224	21010	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.84→68.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5968	0	134	0	6102

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6173
X-RAY DIFFRACTION	f_angle_d	1.441	8416
X-RAY DIFFRACTION	f_dihedral_angle_d	18.092	952
X-RAY DIFFRACTION	f_chiral_restr	0.069	1017
X-RAY DIFFRACTION	f_plane_restr	0.012	1096

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 (%)
2.84-2.99	0.3714	147	0.3025	2791	X-RAY DIFFRACTION	95
2.99-3.18	0.3346	148	0.2799	2817	X-RAY DIFFRACTION	95
3.18-3.42	0.3002	146	0.2536	2808	X-RAY DIFFRACTION	95
3.42-3.77	0.3076	153	0.2245	2819	X-RAY DIFFRACTION	95
3.77-4.31	0.2863	135	0.2057	2866	X-RAY DIFFRACTION	96
4.31-5.43	0.2647	156	0.1827	2865	X-RAY DIFFRACTION	95
5.44-68.31	0.2906	151	0.2085	3008	X-RAY DIFFRACTION	95

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	7.9606	-1.2519	-2.7125	0.3307	-0.3789	3.0098	0.3783	-0.4883	-0.2637	-0.0309	-0.1349	0.1372	0.2351	0.2335	-0.2905	0.7025	0.0292	0.0002	0.3701	-0.03	0.3148	73.3238	20.3436	32.5988
2	6.7148	0.0664	0.0295	3.8861	-0.1876	2.8765	0.2365	0.2461	-0.4623	-0.7405	-0.1133	-0.1949	0.8461	0.414	-0.1081	0.7946	0.0576	-0.0207	0.4891	-0.0626	0.2853	72.0153	18.8167	26.0678
3	4.6646	-0.8503	-0.3102	1.6994	0.432	1.3746	-0.1851	0.189	0.8355	0.1418	0.1229	0.1564	-0.2975	0.0099	0.1235	0.8365	0.0414	-0.1139	0.5079	0.0097	0.1121	74.3095	31.8893	26.3188
4	2.2414	2.7442	-1.9809	5.0742	0.5485	6.1656	0.3804	0.0031	0.318	1.9193	-0.4191	-0.0136	-0.2502	0.8933	-0.0734	1.1624	-0.0244	-0.0491	0.5387	0.0863	0.4345	66.4804	36.2095	42.3578
5	1.1418	-1.0274	0.6155	6.3828	0.4111	3.3036	-0.1829	-1.1768	0.1723	1.7359	0.9732	-0.4038	-0.7553	-0.5585	-0.4632	1.5201	-0.1868	0.2505	0.8014	-0.0291	0.553	60.3786	27.7373	46.8394
6	0.9856	-0.8855	-2.4019	4.4199	1.1008	6.0189	-0.3669	0.1412	-0.2405	1.2069	-0.1684	0.7038	0.1105	-0.1037	0.5435	0.8068	-0.2301	0.237	0.6603	0.0548	0.6039	57.367	21.1829	39.9455
7	3.1283	-1.2977	-0.5684	7.1907	-0.6108	0.5012	0.354	0.4924	0.2531	-0.0008	-0.7592	-0.6533	-0.0774	0.0707	0.4162	0.69	-0.1109	-0.1311	0.4868	0.0185	0.3032	95.7846	20.2103	39.6848
8	5.1302	-1.3135	-1.8562	2.5358	0.6811	2.7307	0.1697	-0.1359	-0.7519	-0.7819	-0.2692	0.1578	-0.1678	0.3624	0.3645	0.814	-0.1754	-0.0518	0.4669	0.0287	0.4373	100.3184	6.9401	41.531
9	2.5724	4.0917	-0.0083	8.7169	1.6131	1.1091	0.0532	-0.544	0.0381	1.0913	-0.0159	0.3314	0.2997	-0.1993	-0.1941	0.721	-0.0966	-0.0738	0.614	-0.0344	0.2281	92.9522	13.1099	44.9845
10	5.6454	-3.9231	1.2789	4.6024	-0.1019	2.6107	-0.1773	-0.3567	0.866	0.3117	-0.0127	-1.1111	-0.5136	-0.2844	0.0731	0.8169	-0.1811	-0.1212	0.496	0.0368	0.4051	97.081	29.8409	40.8372
11	7.2304	-0.8646	-0.8473	8.5992	2.4585	3.242	-1.2371	0.0932	-0.4483	-0.8723	1.1842	-0.9451	0.3098	0.5738	-0.1395	0.6129	-0.0998	0.1537	0.6463	0.0017	0.4571	114.4214	18.6317	42.6642
12	0.8929	-1.7919	-0.4301	5.2674	2.6044	2.0471	0.2372	1.1743	0.693	-2.4823	-0.3812	-0.7305	-1.2817	0.693	0.1852	1.4725	-0.1059	-0.1147	1.8136	0.5925	0.4552	106.2621	23.4878	18.428
13	5.5345	-3.2003	2.115	3.3232	0.871	4.3496	0.0662	0.9093	0.3932	0.0855	0.288	-0.215	-0.8791	1.1856	-0.3291	0.8182	-0.2465	0.3062	0.7054	0.1143	1.3053	112.66	19.5351	28.4021
14	1.0692	1.1789	-0.2419	1.358	-0.7056	3.5448	-0.9753	-1.4281	0.1269	-1.6727	0.4311	-0.5554	-0.1109	-1.0051	0.2992	1.5015	0.2637	0.1571	1.2233	0.1019	0.4209	95.3274	10.0104	23.0357
15	1.5033	0.825	-2.2512	5.0613	-1.6167	7.4774	-1.4906	1.2486	-0.8813	-0.4416	0.5413	-1.0195	1.3712	0.2177	0.7291	1.2286	-0.0246	0.6526	0.9188	0.0037	0.9869	110.7952	9.4501	24.5085
16	1.2358	2.973	-0.4003	8.0114	-2.0741	2.5329	-0.9262	0.6375	-1.7112	-0.2061	-0.4295	-1.8901	0.3854	0.0643	-0.1997	1.3428	-0.2981	0.6525	0.6093	-0.5013	0.9366	109.5673	4.4223	34.3046
17	1.5711	-1.0067	-0.1778	4.0613	2.5927	3.4613	-0.3235	0.1085	-0.2458	-0.5437	0.4605	0.1562	-0.4348	-0.3864	-0.226	0.5822	0.169	0.0568	0.7882	0.0625	0.3635	80.7827	18.9612	5.3091
18	4.2995	0.6282	1.0822	6.4732	3.0712	5.7292	-0.231	0.7515	0.215	-0.1721	0.0295	1.23	-0.5046	-0.5605	0.2701	0.5224	-0.0253	0.0393	1.1191	-0.0605	0.4448	72.3345	11.2359	2.4951
19	2.712	2.7683	-1.0776	4.7952	1.0301	2.2757	-0.1271	-0.6372	-0.3901	0.301	-0.1643	-0.4662	-0.1462	0.2213	0.332	0.5773	0.0261	0.0609	0.96	0.0534	0.3278	82.5693	14.2351	10.9658
20	2.908	0.0938	0.0808	9.3502	1.1658	2.6593	-1.5098	0.515	0.0998	0.7982	1.7584	-1.0538	-0.2815	1.1835	-0.0619	0.574	0.1036	-0.0785	0.9893	0.0081	0.2286	93.2015	23.276	11.2613
21	2.0415	-0.4429	-0.8675	1.8544	1.1921	1.4605	-0.1226	-0.4911	-0.6625	0.3894	0.0037	-0.244	-0.0154	0.424	-0.0965	0.6098	0.0886	0.0318	0.8385	0.0783	0.3297	93.8942	6.8603	-0.6217
22	7.5629	-1.1814	-0.5946	5.1515	3.2414	2.0513	-0.3999	1.3427	0.8207	-0.1708	0.6057	-0.2442	0.6099	-0.4491	-0.0141	0.7149	-0.0564	0.2125	1.128	0.0229	0.2532	88.5685	5.1034	-5.9641
23	0.5745	0.7156	0.3767	0.8512	0.4319	0.2075	-0.9434	1.0316	-0.6131	-0.6524	1.1502	0.0619	0.5732	-1.2777	-0.0518	1.1329	-0.1156	-0.0597	1.1116	0.0066	0.3725	86.0234	1.2451	-10.3353
24	4.0313	-1.4019	-0.0213	2.7673	2.4585	6.1235	-0.2687	-0.1917	-1.911	0.1051	0.1407	0.5833	1.0956	-0.8559	0.7531	0.7587	-0.4919	0.2775	1.313	-0.1075	0.7551	79.4448	-1.6874	-2.5933
25	3.0704	0.0517	0.6697	3.2682	-0.4596	1.8867	-0.3896	0.2078	0.049	0.0692	0.7395	1.4766	-0.9116	-0.1182	0.035	0.692	-0.0419	-0.2201	0.598	0.4642	1.1603	63.6517	50.251	-8.7887
26	2.63	-2.0332	-0.8073	2.0612	0.6213	0.5841	-1.0379	-0.3502	0.0365	1.0516	0.7165	-0.1055	0.4247	-0.0953	-0.0258	0.8193	0.1075	-0.1755	0.555	0.0599	0.4346	84.9527	31.8761	-1.3193
27	5.8137	1.4701	-1.9607	2.0062	0.7627	2.4631	-0.6374	0.7461	0.093	-0.335	0.4712	0.187	-0.2137	-0.1476	0.1833	0.7321	-0.1327	-0.1178	0.643	0.1154	0.3115	71.4249	41.5468	-9.3051
28	2.9779	-0.1559	-0.1966	2.2502	0.8473	0.4069	-0.114	-0.1242	0.8445	0.5396	-0.7651	-0.2803	-0.2817	0.4247	0.1374	0.7644	-0.0611	-0.1549	0.7744	0.1975	0.4744	80.9708	45.502	-3.7056
29	1.2847	-0.8923	0.1201	3.3973	-0.9541	0.2639	-0.3524	-0.1546	0.2942	-0.4049	0.1249	-1.8477	0.6811	-0.5886	0.1768	0.5734	-0.0282	0.0066	0.8116	0.0002	0.5907	98.4749	27.4775	-2.2628
30	3.947	-2.0229	1.1024	3.4505	-0.1811	1.4096	-0.1669	-0.5282	1.1133	0.3655	-0.6432	-0.9117	-0.843	0.983	0.3508	0.4321	0.039	-0.1457	0.7972	0.1074	0.7442	86.0085	52.5166	-6.0043
31	1.9263	-0.5437	0.7309	4.1326	-3.451	6.7429	-0.0385	-0.2759	0.1513	0.3584	-0.0051	-0.4803	-0.0498	-0.2321	0.1494	0.8632	-0.1125	-0.1352	0.5074	0.0434	0.7634	76.4783	55.7584	0.1804
32	3.2532	-1.067	-2.6454	2.0296	1.9417	2.8183	0.4472	0.7796	0.6223	-0.1043	1.2879	0.4236	-0.1904	-0.1506	-1.2367	1.422	0.2975	-0.0401	1.0863	0.0848	0.5168	69.0152	40.8707	14.8565
33	5.978	-0.0979	0.8984	0.1904	0.5591	1.7952	0.2125	-0.8066	1.2609	2.3193	0.2612	0.3232	-0.4072	-0.3808	0.0524	1.3301	0.0555	0.0778	0.6854	-0.199	0.5791	67.8911	54.9548	9.4981
34	7.2791	2.0069	-0.0642	2.4363	1.157	3.8294	0.3175	-0.6737	1.3695	1.2532	-0.7709	-0.1168	-0.773	-0.2804	0.1577	0.5706	0.0474	-0.0777	0.5998	-0.1101	0.5892	63.1745	53.112	1.0114

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 185 through 228 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 229 through 269 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 270 through 333 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 334 through 381 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 382 through 393 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 394 through 412 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 185 through 215 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 216 through 237 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 238 through 255 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 256 through 309 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 310 through 333 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 334 through 344 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 345 through 361 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 362 through 377 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 378 through 393 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 394 through 412 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 185 through 215 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 216 through 247 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 248 through 284 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 285 through 319 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 320 through 354 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 355 through 381 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 382 through 393 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 394 through 412 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 184 through 196 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 197 through 215 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 216 through 269 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 270 through 284 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 285 through 303 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 304 through 320 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 321 through 361 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 362 through 377 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 378 through 393 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 394 through 412 )

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