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

ID or keywords:

Entry

Database: PDB / ID: 8owq

Title

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and 2-(1-(3,4-dihydroxyphenyl)-5-phenyl-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 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: 2.106 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 28, 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	8owq.cif.gz	338 KB	Display	PDBx/mmCIF format
PDB format	pdb8owq.ent.gz	273.7 KB	Display	PDB format
PDBx/mmJSON format	8owq.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/8owq ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8owq	HTTPS FTP

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Related structure data

Related structure data	8ow5C 8owbC 8owpC 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

103 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
Evidence: gel filtration
52.1 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
51.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.200, 78.472, 150.060
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-W4X / 2-[1-[3,4-bis(oxidanyl)phenyl]-5-phenyl-indol-3-yl]-2-oxidanylidene-ethanoic acid Mass: 373.358 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₂H₁₅NO₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.32 Å³/Da / Density % sol: 47.05 %
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: Jun 25, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.106→150.06 Å / Num. obs: 54197 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC_1/2: 0.997 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.042 / R_rim(I) all: 0.117 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.11→2.22 Å / % possible obs: 100 % / Redundancy: 7.5 % / R_merge(I) obs: 0.791 / Num. measured all: 58720 / Num. unique obs: 7832 / CC_1/2: 0.765 / R_pim(I) all: 0.312 / R_rim(I) all: 0.852 / Net I/σ(I) obs: 2.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.106→69.348 Å / Cross valid method: THROUGHOUT / σ(F): 27.38 / Phase error: 28 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2556	2712	5.01 %
R_work	0.2066	-	-
obs	0.2109	54124	99.85 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.106→69.348 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6098	0	288	454	6840

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6479
X-RAY DIFFRACTION	f_angle_d	1.008	8823
X-RAY DIFFRACTION	f_dihedral_angle_d	14.33	3787
X-RAY DIFFRACTION	f_chiral_restr	0.053	1021
X-RAY DIFFRACTION	f_plane_restr	0.006	1143

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 (%)
2.1064-2.1446	0.3572	149	0.2943	2667	X-RAY DIFFRACTION	95
2.1446-2.1858	0.35	155	0.2982	2654	X-RAY DIFFRACTION	94
2.1858-2.2304	0.3323	140	0.2835	2667	X-RAY DIFFRACTION	95
2.2304-2.2789	0.2859	127	0.2725	2671	X-RAY DIFFRACTION	95
2.2789-2.3318	0.3453	128	0.281	2705	X-RAY DIFFRACTION	95
2.3318-2.3901	0.3339	153	0.2704	2656	X-RAY DIFFRACTION	95
2.3901-2.4546	0.3567	142	0.2686	2702	X-RAY DIFFRACTION	95
2.4546-2.5267	0.3144	119	0.2623	2695	X-RAY DIFFRACTION	96
2.5267-2.6081	0.2986	122	0.2427	2691	X-RAY DIFFRACTION	96
2.6081-2.7012	0.2899	124	0.2307	2711	X-RAY DIFFRACTION	96
2.7012-2.8091	0.302	149	0.2282	2664	X-RAY DIFFRACTION	95
2.8091-2.9367	0.317	155	0.2165	2677	X-RAY DIFFRACTION	94
2.9367-3.0911	0.2879	165	0.2122	2666	X-RAY DIFFRACTION	94
3.0911-3.2841	0.241	157	0.2049	2709	X-RAY DIFFRACTION	94
3.2841-3.5366	0.2463	140	0.1889	2717	X-RAY DIFFRACTION	95
3.5366-3.8907	0.2315	152	0.1684	2709	X-RAY DIFFRACTION	94
3.8907-4.4493	0.1794	134	0.1533	2754	X-RAY DIFFRACTION	95
4.4493-5.5894	0.1776	135	0.1612	2777	X-RAY DIFFRACTION	95
5.5894-21.5174	0.2258	154	0.2047	2857	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	2.7474	-0.6515	-0.3895	2.8657	-0.2055	2.351	0.0814	-0.2904	0.6468	0.1177	0.0585	0.3609	-0.6097	-0.197	-0.1084	0.2739	0.0608	0.0978	0.2502	-0.0023	0.4654	-3.4649	-1.4948	-6.8276
2	1.6888	0.5055	-0.1134	2.4228	-0.4389	1.6356	0.032	-0.0317	0.0152	0.0085	-0.022	0.2753	0.0795	-0.2017	-0.0311	0.1452	-0.0299	-0.0052	0.187	0.0165	0.2532	0.1415	-17.3327	-6.8949
3	1.5241	0.3849	-0.5831	3.9483	-0.1958	1.9902	0.0888	0.1991	-0.0681	0.0188	-0.127	0.0077	0.038	0.0314	0.0027	0.1495	-0.0226	0.0041	0.1815	0.0192	0.2491	8.4409	-13.4485	-8.7938
4	3.5674	1.8457	-0.3315	4.238	-0.6858	3.2316	-0.3236	0.3459	-1.1408	-1.2302	0.1802	-1.0306	0.6428	0.306	-0.0246	0.689	0.1709	0.1707	0.3871	-0.0129	0.515	13.451	-37.6287	-11.329
5	0.6163	0.6183	-0.3406	5.3015	-0.6873	2.5738	-0.0796	-0.1774	-0.0841	-0.1478	-0.24	-0.3949	0.2259	0.1618	0.2718	0.1695	-0.0062	0.024	0.2095	0.0552	0.2838	15.9141	-12.2435	-10.8359
6	2.0665	0.2033	0.5058	2.7021	-1.1414	4.9172	0.0185	-0.1117	0.0912	0.1555	-0.0049	0.0072	-0.1527	-0.3042	0.1513	0.1778	-0.0083	0.0253	0.1158	-0.0164	0.2838	12.3728	-6.131	-2.675
7	2.8763	0.223	1.5334	3.6221	-1.4627	1.5359	0.1087	-0.3991	0.1718	0.3402	-0.177	-0.1237	-0.1267	-0.1606	0.0386	0.195	-0.0306	0.0004	0.2147	-0.0326	0.3165	14.0565	-5.6997	5.0465
8	1.7935	1.283	-2.1174	1.5359	-1.7576	2.8346	0.1285	0	0.674	0.2756	0.1466	0.6095	-0.0472	-0.2714	-0.2951	0.3603	-0.0765	0.0831	0.2973	-0.0921	0.3486	7.2766	-1.1375	9.0127
9	5.5628	0.6787	0.685	1.7516	0.5975	2.0149	0.3265	-0.309	0.9384	0.4343	-0.0618	0.3217	-0.4733	-0.0287	-0.0058	0.2971	0.034	0.0853	0.3044	-0.1296	0.4962	0.8659	0.6535	1.8615
10	1.3002	-0.4536	0.1957	1.4563	-0.6878	1.6177	0.0484	-0.0257	-0.127	-0.0447	0.0264	0.1014	0.0361	-0.1295	-0.0416	0.1717	0.0188	0.0029	0.1654	0.0416	0.2842	-1.9345	-38.9671	4.9473
11	1.6536	0.4035	0.5619	1.7897	-0.5744	1.2489	0.0293	-0.0587	-0.2015	0.005	-0.0854	-0.2806	0.0467	0.1519	0.0729	0.2103	0.0162	-0.0282	0.1714	0.0572	0.3457	0.5986	-41.5083	7.195
12	3.2504	-0.8661	2.5304	1.7815	-2.2632	6.4201	0.3462	0.6072	-0.5477	-0.4405	-0.259	-0.2594	0.8961	0.4798	-0.0521	0.3622	0.0945	-0.0587	0.2877	-0.0318	0.5621	-2.5127	-55.2579	-2.8019
13	3.96	-5.2579	-3.6124	7.6978	4.3233	3.5646	0.9016	0.3898	-0.6459	-1.332	-0.4187	-0.7532	1.3061	-0.0672	-0.1825	0.7393	0.0035	-0.2636	0.2851	-0.1014	0.9657	-12.2865	-55.2528	-8.2987
14	1.9903	-2.2105	-0.0381	7.849	-1.366	4.489	0.2404	-0.0544	-0.7197	0.1013	-0.1605	-0.1565	0.5838	0.1202	-0.1155	0.2386	-0.0326	-0.1233	0.2281	0.0232	0.5286	-15.5824	-53.3066	0.7045
15	6.8019	-0.7804	-1.3917	2.5672	0.8088	2.9957	0.1541	0.3717	0.7017	-0.1038	-0.1688	0.3672	-0.0427	-0.6092	0.0261	0.2568	0.0179	0.0346	0.2411	0.0151	0.3732	-18.4257	-20.9307	-30.9914
16	4.7122	-0.2135	-0.8406	0.8942	0.2415	1.459	-0.0512	-0.1973	0.1314	-0.0086	0.0341	-0.0928	-0.0726	0.0819	0.0111	0.2601	-0.012	0.0248	0.1382	-0.0088	0.2258	-3.5246	-26.1945	-30.1672
17	6.8312	0.4608	-2.8648	3.3057	0.6812	3.9261	0.1399	-0.5318	-0.426	0.2436	-0.3959	-0.7567	0.1283	0.8667	0.1057	0.3371	0.0548	0.0907	0.3938	0.2429	0.5771	9.1721	-42.0465	-27.2973
18	3.5146	-0.1129	-1.7419	1.0343	1.3604	3.9959	-0.2927	-0.3144	-0.3959	-0.1772	0.0384	0.0475	0.3771	-0.2568	0.2103	0.3399	-0.016	0.0896	0.1929	-0.0164	0.3386	-17.605	-36.648	-24.1166
19	2.0314	-2.2744	-1.7947	2.9587	2.8698	3.5749	0.0666	-0.0742	-0.0139	-0.076	0.0456	-0.0897	0.0199	0.0006	0.0584	0.2326	-0.034	0.0393	0.179	-0.0032	0.3	-12.2593	-39.1255	-42.8757
20	3.6364	-1.0911	-0.132	0.4419	0.6933	3.9652	0.2022	0.3327	0.6921	0.0239	-0.058	0.4512	-0.0791	-0.3919	-0.2101	0.3085	-0.0162	0.0217	0.2936	0.0706	0.3725	-18.3055	-31.6516	-47.006
21	3.584	-0.211	1.067	6.95	1.9168	5.5123	0.11	0.2063	0.0731	-0.3759	-0.0576	0.6034	-0.2537	-0.5641	0.3257	0.3187	0.0698	-0.0666	0.216	-0.0039	0.3586	-20.4279	-25.3971	-40.0435
22	2.5811	1.0575	-0.7285	1.4119	0.3992	1.6705	0.0229	-0.1297	0.0924	-0.0525	0.0078	-0.1273	-0.0494	0.1087	-0.0104	0.1886	0.0414	0.0321	0.1886	-0.0202	0.3254	19.2794	-22.7441	-41.1314
23	2.3824	0.956	-0.9094	1.73	-0.1531	1.6192	0.0233	-0.066	-0.1348	-0.0964	0.0032	-0.0988	0.0522	0.0219	-0.0226	0.2039	0.0374	0.0189	0.2187	-0.0616	0.307	22.1597	-25.1831	-43.4228
24	0.0792	0.1381	-0.6715	1.3888	-0.3145	6.1682	0.0261	-0.0769	-0.1487	0.1513	-0.06	-0.3958	0.2566	0.3348	-0.0144	0.2037	0.0428	-0.0428	0.3615	-0.0581	0.5164	35.3742	-24.7095	-32.449
25	5.2917	-1.6155	-4.7266	0.8133	1.7166	4.5023	0.581	0.4679	0.0731	-0.0144	-0.1823	-0.3494	-0.3803	-0.1297	-0.3496	0.1995	0.0186	-0.0201	0.4113	-0.0369	0.3999	25.0167	-15.527	-27.3652
26	0.2153	-0.176	-0.7079	1.5896	-0.7041	3.1553	0.1176	-0.3364	-0.0622	0.194	0.202	-0.7131	-0.4841	0.8039	-0.2893	0.2797	0.0004	-0.0148	0.4799	-0.1919	0.6096	33.0577	-11.822	-30.1043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 184 through 196 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 197 through 267 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 268 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 381 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 382 through 393 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 394 through 412 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 184 through 215 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 216 through 319 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 320 through 381 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 382 through 393 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 394 through 412 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 184 through 196 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 197 through 284 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 285 through 309 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 310 through 327 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 328 through 381 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 382 through 393 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 394 through 412 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 184 through 215 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 216 through 319 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 320 through 354 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 355 through 371 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 372 through 412 )

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