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

ID or keywords:

Entry

Database: PDB / ID: 8owp

Title

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and 2-(1-(4-hydroxyphenyl)-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: 1.993 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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PDBx/mmCIF format	8owp.cif.gz	330.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8owp.ent.gz	267.7 KB	Display	PDB format
PDBx/mmJSON format	8owp.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/8owp ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8owp	HTTPS FTP

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Related structure data

Related structure data	8ow5C 8owbC 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
Evidence: gel filtration
51.3 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 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.816, 76.409, 143.193
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#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)

#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)

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Non-polymers , 5 types, 352 molecules

#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-W52 / 2-[1-(4-hydroxyphenyl)-5-phenyl-indol-3-yl]-2-oxidanylidene-ethanoic acid Mass: 357.359 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₂H₁₅NO₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.09 Å³/Da / Density % sol: 41.22 %
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: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.99→76.41 Å / Num. obs: 54112 / % possible obs: 93.9 % / Redundancy: 7.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.041 / R_rim(I) all: 0.11 / Net I/σ(I): 12.2 / Num. measured all: 387121
Reflection shell	Resolution: 1.99→2.1 Å / % possible obs: 80.6 % / Redundancy: 7 % / R_merge(I) obs: 0.84 / Num. measured all: 46982 / Num. unique obs: 6677 / CC_1/2: 0.724 / R_pim(I) all: 0.334 / R_rim(I) all: 0.906 / Net I/σ(I) obs: 2.2

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2947: ???)	refinement
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.993→53.818 Å / Cross valid method: THROUGHOUT / σ(F): 21.5 / Phase error: 31.31 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2538	2825	5.23 %
R_work	0.1985	-	-
obs	0.2033	54039	93.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.993→53.818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5988	0	205	340	6533

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6274
X-RAY DIFFRACTION	f_angle_d	1.163	8546
X-RAY DIFFRACTION	f_dihedral_angle_d	13.857	3714
X-RAY DIFFRACTION	f_chiral_restr	0.057	1016
X-RAY DIFFRACTION	f_plane_restr	0.008	1114

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 (%)
1.9935-2.0278	0.3254	159	0.3016	2660	X-RAY DIFFRACTION	94
2.0278-2.0647	0.3472	86	0.2953	1916	X-RAY DIFFRACTION	68
2.0647-2.1044	0.3319	98	0.2825	1961	X-RAY DIFFRACTION	69
2.1044-2.1473	0.3129	146	0.2773	2673	X-RAY DIFFRACTION	95
2.1473-2.1939	0.3354	147	0.2872	2706	X-RAY DIFFRACTION	95
2.1939-2.2449	0.3246	90	0.2772	2110	X-RAY DIFFRACTION	74
2.2449-2.301	0.3111	120	0.2841	2180	X-RAY DIFFRACTION	77
2.301-2.3631	0.3198	151	0.2696	2666	X-RAY DIFFRACTION	95
2.3631-2.4326	0.3405	115	0.2699	2740	X-RAY DIFFRACTION	96
2.4326-2.511	0.3333	157	0.2665	2695	X-RAY DIFFRACTION	94
2.511-2.6006	0.3184	125	0.2596	2726	X-RAY DIFFRACTION	96
2.6006-2.7046	0.3243	114	0.2555	2134	X-RAY DIFFRACTION	74
2.7046-2.8274	0.3078	165	0.2348	2693	X-RAY DIFFRACTION	94
2.8274-2.9761	0.2931	150	0.2258	2705	X-RAY DIFFRACTION	95
2.9761-3.1621	0.259	143	0.2202	2753	X-RAY DIFFRACTION	95
3.1621-3.4054	0.2503	165	0.1921	2702	X-RAY DIFFRACTION	94
3.4054-3.7466	0.2216	162	0.162	2730	X-RAY DIFFRACTION	94
3.7466-4.2852	0.2064	154	0.1506	2778	X-RAY DIFFRACTION	95
4.2852-5.3857	0.1977	161	0.128	2785	X-RAY DIFFRACTION	94
5.3857-21.9364	0.223	145	0.1672	2926	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	0.3022	0.4655	0.4917	1.6869	0.0925	2.3035	0.0781	0.2152	0.1361	0.0223	-0.037	-0.1432	0.1161	-0.044	-0.0485	0.3376	-0.0136	-0.0263	0.0821	0.03	0.1468	0.7663	22.1749	-30.5375
2	4.6891	-1.2548	0.3464	3.0639	-0.3084	2.5012	-0.0121	0.1309	-0.5273	-0.2519	-0.0175	-0.0024	0.3032	-0.0007	-0.1115	0.4378	-0.0429	-0.0544	0.1629	-0.0208	0.2828	10.8317	14.6693	-33.1152
3	3.9985	-0.9895	0.2784	2.5662	0.7816	1.2252	-0.088	-0.2084	-0.2482	0.1623	0.0098	0.0348	0.1544	-0.2424	0.064	0.3712	-0.026	-0.0138	0.2228	0.0409	0.1539	4.0248	22.4415	-26.1606
4	6.1736	-0.2475	-1.6086	0.693	0.1815	2.396	-0.1526	-0.3248	0.4458	-1.011	0.2878	1.1388	0.0582	-1.1837	-0.058	0.525	-0.016	-0.234	0.4937	-0.037	0.444	-18.8954	34.4012	-23.7564
5	7.7324	0.5247	0.4866	0.1443	0.0118	1.0527	0.0838	-0.2635	0.5485	-0.0281	-0.1147	-0.037	-0.4408	0.0083	0.0761	0.3912	-0.0116	-0.0911	0.1905	-0.0158	0.2268	7.4849	35.4305	-25.1403
6	1.7072	-0.362	0.684	1.4696	-1.3846	3.3776	-0.0206	-0.1367	0.2237	0.0757	-0.1043	-0.1366	0.0723	-0.2201	0.1532	0.3045	-0.0219	-0.0015	0.1951	-0.0025	0.1967	12.4505	32.8517	-33.9521
7	5.4747	-0.4741	3.3633	4.9024	-2.5698	3.1343	-0.39	0.2612	0.5296	0.2236	-0.0852	-0.4266	-0.599	-0.0264	0.3726	0.3281	0.0252	-0.0201	0.1955	-0.0137	0.2409	11.876	39.0982	-40.6387
8	6.9375	-0.5999	-2.6273	1.9504	0.6082	2.88	-0.0065	0.321	-0.6271	-0.4754	0.0835	0.1019	0.0107	0.0443	0.0099	0.4664	-0.0122	-0.0336	0.1664	0.0035	0.1797	13.9377	29.5805	-42.427
9	6.5742	7.034	4.0762	9.3733	4.8979	4.6399	0.0898	-0.1724	-0.4011	-0.8036	-0.1423	-0.466	-0.3252	0.0533	-0.0385	0.4063	0.1108	-0.0046	0.3999	-0.0504	0.2021	17.0103	27.0237	-45.6601
10	7.7041	0.9566	1.0557	7.6217	0.8578	7.0278	-0.5066	0.0775	-0.3485	-0.5368	0.2739	-0.6134	-0.6078	0.6282	0.1103	0.3744	0.0477	0.0548	0.2256	0.0171	0.2373	18.7653	20.3031	-39.6402
11	3.7344	1.934	0.8286	1.6833	0.2777	1.4552	0.1038	-0.1996	-0.1746	-0.0967	-0.1624	0.1655	-0.0859	-0.1827	0.0569	0.2978	0.0445	-0.0364	0.1721	-0.0212	0.2545	-19.8539	18.028	-39.4061
12	1.8308	0.6897	0.1154	3.6911	-0.2461	0.8282	-0.0275	0.0328	0.0044	-0.2433	-0.0391	0.0283	-0.0246	0.024	0.0575	0.3607	0.0496	-0.052	0.2626	-0.0129	0.1934	-22.3385	12.6459	-44.0034
13	2.6159	1.0573	-0.1353	2.6919	-0.4093	0.8111	0.1297	-0.1764	0.4661	0.1324	-0.1901	0.0024	-0.1847	0.0797	0.0778	0.3834	0.0313	-0.0435	0.2304	-0.0201	0.2803	-17.4671	31.1308	-37.38
14	8.6731	5.8049	3.3125	4.067	1.8793	1.7928	-0.0623	-0.2245	0.6588	0.125	-0.1466	0.3572	-0.1841	-0.3151	0.2966	0.3822	0.1013	-0.0483	0.2876	-0.029	0.3721	-31.0969	27.9605	-38.7639
15	4.2881	0.401	3.2993	5.255	-0.3622	7.8118	0.1335	-0.2042	0.0489	0.0662	0.3359	0.2057	0.3226	-0.1889	-0.3319	0.2129	0.0243	0.0161	0.2904	-0.0142	0.3708	-36.4309	16.2596	-39.9422
16	2.4436	-1.8643	0.5873	2.4503	-3.4447	9.6738	0.0109	-0.8537	0.7655	0.9853	0.0463	0.4574	-0.022	-0.6234	-0.3023	0.5062	0.0562	0.0891	0.6146	-0.1066	0.5184	-35.4341	15.906	-26.9552
17	1.7446	-0.8869	-2.8647	9.6234	-0.1955	8.0883	-0.5412	-1.827	0.8474	0.6499	0.6944	0.9944	0.4599	-0.1397	-0.0912	0.4617	0.007	0.0348	0.7255	-0.0875	0.4999	-33.8224	7.4187	-24.7738
18	6.3197	-4.6284	1.8702	5.7027	-2.167	6.1374	0.2459	-0.5461	-1.0385	0.0327	0.2313	0.8889	0.1979	-0.5953	-0.3198	0.3256	-0.0199	-0.0196	0.3125	0.0175	0.3452	-33.1881	3.6259	-34.0801
19	0.3739	0.6877	0.0585	1.606	0.484	1.1908	0.0072	0.0835	-0.0148	0.1247	-0.0154	-0.4007	0.0747	-0.0078	-0.0133	0.2904	-0.0946	0.0497	0.4311	-0.0408	0.2958	-3.1383	17.1288	-4.9674
20	1.4047	-0.8951	0.2438	3.5229	-0.23	2.7827	0.0148	-0.0225	0.1521	-0.0591	0.0583	-0.4605	-0.1852	0.4288	-0.0411	0.2962	-0.0838	0.0639	0.4585	-0.0673	0.2703	-0.9503	11.6266	-7.0748
21	2.1267	-1.8921	0.3306	7.8781	-0.5683	3.1416	-0.1539	0.0436	0.2046	-0.4068	0.0581	1.1372	-0.6883	-0.6664	0.0021	0.3094	0.0224	-0.086	0.4884	-0.0246	0.3684	-17.3549	35.6025	-11.38
22	0.175	-0.0899	-0.0944	7.1293	1.1477	0.6885	-0.2114	-0.0049	-0.045	-0.5428	0.0402	0.8117	0.1874	-0.5798	0.1305	0.3508	-0.1246	0.0221	0.5629	-0.119	0.294	-16.3589	10.532	-10.5222
23	0.4959	-0.5376	-1.4028	1.666	1.789	6.21	-0.0322	-0.0029	-0.0199	-0.1836	0.2612	0.0691	-0.2533	0.2748	-0.2555	0.3378	-0.0428	0.0518	0.366	-0.0275	0.2756	-13.9818	5.4179	-1.9008
24	1.0085	-0.0812	-2.1963	2.0556	1.3542	5.8673	-0.0349	0.2481	-0.0916	-0.0611	0.1491	0.0983	-0.0164	-0.6488	-0.1007	0.282	-0.0375	0.0122	0.3461	0.021	0.244	-20.3695	6.3554	4.6036
25	8.0662	0.6154	-1.489	7.8958	-2.3354	6.1504	-0.2199	-0.8402	0.1239	0.4941	0.1572	-0.6845	0.3599	0.1881	0.1822	0.3074	0.0239	0.015	0.3723	-0.0381	0.3102	-10.5381	2.4608	7.3923
26	6.2579	-2.4214	-0.6781	7.5565	4.698	3.0449	-0.4566	-0.1546	0.2759	0.3388	0.1511	0.6886	0.7006	0.041	0.0955	0.4491	-0.0928	-0.0295	0.5989	0.2047	0.4597	-1.6377	-1.3405	3.9182
27	3.3065	1.711	1.008	3.1102	1.8738	3.456	-0.0629	-0.1638	0.2796	0.0694	0.1399	-0.106	0.1812	0.0047	-0.0201	0.2897	0.0825	-0.0273	0.2371	-0.0612	0.2318	0.2284	38.2015	3.9603
28	5.3456	0.3745	-1.4607	2.5199	-0.5598	4.9329	-0.2087	-0.132	0.0232	0.0345	0.1038	-0.3088	0.2216	0.3358	0.0135	0.3461	0.1195	-0.0615	0.2403	-0.0582	0.2224	10.8226	40.2614	5.9455
29	1.9135	2.2515	0.5522	4.0768	2.0035	2.0566	-0.0374	-0.064	0.3628	0.1682	-0.1526	0.5717	0.0357	-0.2767	0.1859	0.3419	0.0714	0.0193	0.3095	-0.0437	0.2425	-6.9516	42.8362	6.9827
30	0.7074	-0.021	0.3046	4.2996	2.1631	3.8653	0.081	0.2872	0.1965	-0.624	-0.1024	0.3104	-0.5537	-0.2286	0.0899	0.3921	0.0172	-0.0477	0.3069	0.0603	0.3855	0.4276	51.2582	-6.4952
31	6.6087	-1.2584	1.173	6.8304	-3.3196	3.2191	-0.1626	0.3825	0.8583	-0.2754	0.0375	0.5958	-0.1249	0.1763	0.046	0.3731	-0.0708	-0.0329	0.2854	0.0185	0.3711	11.1824	53.5318	-4.5334

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 236 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 237 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 301 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 302 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 381 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 382 through 393 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 394 through 412 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 185 through 215 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 216 through 284 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 285 through 303 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 304 through 319 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 320 through 342 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 343 through 354 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 355 through 393 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 394 through 411 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 184 through 215 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 216 through 247 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 248 through 319 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 320 through 377 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 378 through 411 )

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