PDB-7yyb: Crystal structure of Mycobacterium abscessus Phosphopantetheine a...

ID or keywords:

Entry

Database: PDB / ID: 7yyb

Title

Crystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Fragment 15

Components

Phosphopantetheine adenylyltransferase

Keywords

TRANSFERASE /

CoaD /

PPAT /

nucleotidyltransferase

Function / homology

Function and homology information

pantetheine-phosphate adenylyltransferase /

pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Mycobacteroides abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.751 Å

Authors

Thomas, S.E. / Coyne, A.G. / Blundell, T.L.

Funding support

United Kingdom, 1items

Citation

Journal: Front Mol Biosci / Year: 2022
Title: Structural Characterization of Mycobacterium abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications for Fragment-Based Drug Design.
Authors: Thomas, S.E. / McCarthy, W.J. / El Bakali, J. / Brown, K.P. / Kim, S.Y. / Blaszczyk, M. / Mendes, V. / Abell, C. / Floto, R.A. / Coyne, A.G. / Blundell, T.L.

History

Deposition	Feb 17, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 29, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7yyb.cif.gz	196.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7yyb.ent.gz	157.4 KB	Display	PDB format
PDBx/mmJSON format	7yyb.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/yy/7yyb ftp://data.pdbj.org/pub/pdb/validation_reports/yy/7yyb	HTTPS FTP

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Related structure data

Related structure data	7ywmC 7yxzC 7yy0C 7yy1C 7yy2C 7yy3C 7yy4C 7yy5C 7yy6C 7yy7C 7yy8C 7yy9C 7yyaC 7yycC 5o06S S: Starting model for refinement 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

Deposited unit

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

hetero molecules

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

1

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

hetero molecules

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
106 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.295, 125.184, 119.002
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-332- HOH

#1: Protein	Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT Mass: 17476.887 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase
#2: Chemical	ChemComp-QX4 / 4-hydroxy-6-methyl-2H-1-benzopyran-2-one Mass: 176.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.71 Å³/Da / Density % sol: 54.61 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium bromide, 20-24 % PEG3350, 0.1 M Bis-Tris propane pH 6.5

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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: 0.9173 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9173 Å / Relative weight: 1

Reflection

Resolution: 1.75→65.15 Å / Num. obs: 57603 / % possible obs: 100 % / Redundancy: 6.6 % / B_iso Wilson estimate: 23.58 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / R_pim(I) all: 0.024 / R_rim(I) all: 0.063 / Net I/σ(I): 21.1 / Num. measured all: 382395

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.75-2.02	6.7	0.481	133667	19981	0.94	0.2	0.522	4.1	100
3.5-65.15	6.4	0.028	47710	7462	0.999	0.012	0.03	59.9	99.9

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Phasing

Phasing	Method: molecular replacement
Phasing MR	Model details: Phaser MODE: MR_AUTO

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Processing

Software

Name	Version	Classification
Aimless	0.5.1	data scaling
PHASER	2.5.6	phasing
PHENIX	1.9	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5O06

5o06

Resolution: 1.751→65.149 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2034	2804	4.87 %
R_work	0.1758	54754	-
obs	0.1772	57558	99.93 %

Solvent computation

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

Displacement parameters

B_iso max: 108.34 Å² / B_iso mean: 30.0864 Å² / B_iso min: 14.24 Å²

Refinement step

Cycle: final / Resolution: 1.751→65.149 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3527	0	26	289	3842
B_iso mean	-	-	36.46	38.52	-
Num. residues	-	-	-	-	471

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3705
X-RAY DIFFRACTION	f_angle_d	0.989	5051
X-RAY DIFFRACTION	f_chiral_restr	0.043	595
X-RAY DIFFRACTION	f_plane_restr	0.004	659
X-RAY DIFFRACTION	f_dihedral_angle_d	11.676	1338

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.751-1.7809	0.3497	111	0.267	2743	100
1.7809-1.8133	0.2959	109	0.2391	2735	100
1.8133-1.8482	0.2511	124	0.2145	2681	100
1.8482-1.8859	0.2378	134	0.2025	2763	100
1.8859-1.9269	0.2266	144	0.1945	2688	100
1.9269-1.9717	0.2289	121	0.1876	2720	100
1.9717-2.021	0.2331	138	0.174	2727	100
2.021-2.0757	0.2159	165	0.1761	2692	100
2.0757-2.1368	0.1866	133	0.1711	2717	100
2.1368-2.2057	0.1948	160	0.1688	2702	100
2.2057-2.2846	0.1947	144	0.1705	2727	100
2.2846-2.376	0.179	123	0.1695	2754	100
2.376-2.4842	0.2087	168	0.1804	2687	100
2.4842-2.6152	0.2191	168	0.191	2726	100
2.6152-2.779	0.2145	133	0.1849	2739	100
2.779-2.9936	0.2244	140	0.1793	2750	100
2.9936-3.2948	0.1992	152	0.188	2742	100
3.2948-3.7716	0.1971	140	0.1651	2774	100
3.7716-4.7516	0.1711	131	0.1416	2800	100
4.7516-65.149	0.1927	166	0.179	2887	99

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	4.198	0.0554	-0.2745	1.2603	0.3055	3.4862	-0.0617	-0.0982	0.0785	-0.0127	-0.0036	-0.0082	-0.0148	-0.1446	0.0551	0.1809	-0.0255	0.0193	0.1475	0.0037	0.163	-8.5111	-37.4368	-10.8756
2	6.7226	-4.7495	0.4905	5.6695	0.4082	3.6793	-0.1089	-0.1905	-0.4464	0.2496	-0.0545	0.3153	0.3411	-0.3453	0.1898	0.2738	-0.0748	0.032	0.2404	0.0152	0.224	-16.4996	-43.9189	-9.3805
3	3.8467	-1.2035	-0.1805	3.2378	-0.9729	2.4017	-0.024	-0.3174	-0.3934	-0.0254	0.0334	0.0568	0.2573	-0.0014	-0.0096	0.1688	-0.0185	0.0051	0.1895	0.0306	0.1888	-8.2533	-40.176	-4.6316
4	1.3067	0.0608	-0.8781	0.8472	-0.3777	3.5544	0.0504	-0.1244	0.0464	0.0293	-0.0235	0.161	-0.0838	0.0942	-0.0328	0.1629	-0.0356	-0.013	0.1814	-0.0032	0.1937	-4.9479	-29.5467	-8.2092
5	0.8242	-0.8383	-0.7626	2.4006	1.183	3.4202	0.0779	0.0394	0.069	-0.0905	0.0006	0.0428	-0.0737	-0.0846	-0.0439	0.148	-0.023	0.0092	0.1782	0.0119	0.2101	-1.588	-22.6954	-12.6234
6	4.3967	1.5731	-1.1138	1.6847	0.7935	2.6539	-0.3724	0.5031	0.2561	-0.0119	0.2113	0.1491	0.1327	-0.1536	0.1359	0.2016	-0.016	0.0235	0.2312	0.0108	0.1877	-12.4557	-38.5657	-26.2429
7	4.0589	-0.2459	-0.5737	2.131	-0.766	2.8059	0.0177	-0.0543	-0.2196	-0.037	-0.1173	0.3266	0.5703	-0.5469	0.1364	0.3088	-0.0972	0.0547	0.2743	-0.075	0.2724	-18.9754	-46.718	-22.6197
8	2.9869	-0.9273	-0.2992	2.4726	0.1553	1.8151	-0.036	0.0287	0.0722	0.0362	-0.0055	-0.0649	-0.0089	-0.114	0.0474	0.1424	-0.016	-0.0296	0.2667	-0.0153	0.1714	-15.5369	-25.9117	-49.2563
9	6.0319	-1.6793	-3.6353	2.4354	1.549	5.5591	-0.108	0.0312	-0.3026	0.1873	-0.1101	0.1354	0.3804	-0.2988	0.1605	0.1883	-0.0347	-0.0178	0.242	-0.0078	0.1996	-18.0271	-32.9517	-50.4442
10	2.3063	-0.9821	0.9286	8.8876	1.4685	0.7823	-0.0695	-1.0245	0.0073	1.6748	-0.2442	0.5447	0.2415	-0.6224	0.2558	0.4309	-0.063	0.1516	0.7408	-0.0268	0.4191	-30.1746	-24.0966	-36.973
11	5.4386	0.905	-5.1282	2.7852	0.6525	8.6353	-0.2354	0.02	0.6701	0.061	0.1093	0.5726	-0.2825	-0.8653	0.0592	0.1728	0.0354	-0.0622	0.4075	-0.0925	0.327	-28.2387	-23.0355	-49.1677
12	2.3458	-0.2437	-0.4912	1.4741	-1.4575	6.4809	-0.0674	0.0255	-0.2451	-0.1153	-0.0902	0.146	0.0954	-0.2652	0.0992	0.1883	-0.0307	-0.0298	0.2667	-0.0422	0.2383	-21.9962	-30.4501	-51.8973
13	1.9815	0.5761	0.1813	2.5045	0.2469	2.3619	0.0378	-0.047	-0.1244	0.0588	0.043	0.0022	0.1638	-0.2934	-0.0687	0.1549	-0.0066	-0.0137	0.2332	-0.0005	0.1579	-14.9593	-34.2222	-42.5324
14	0.9636	1.1233	-0.5368	3.7701	-2.0417	3.3288	-0.0372	-0.0722	0.038	0.0518	-0.0521	-0.0103	0.0209	0.0189	0.1042	0.1226	0.0028	-0.0027	0.1919	0.0081	0.1678	-8.9145	-34.6965	-36.9492
15	4.4314	-0.4439	-1.5843	3.336	1.5794	3.1281	-0.3411	0.2535	0.0781	-0.0813	0.2651	-0.1479	-0.0353	-0.1346	0.0932	0.2273	0.0032	0.0223	0.2046	-0.0001	0.2479	-10.3536	-14.7647	-44.8613
16	5.999	-1.8047	-0.9322	6.102	0.5451	1.7455	0.0196	-0.5958	0.6621	0.8031	-0.2229	0.1213	-0.0349	-0.5279	0.2224	0.2393	0.0638	-0.0006	0.3613	-0.1125	0.3215	-22.4154	-9.8548	-37.1117
17	4.1791	-0.638	-0.9492	2.586	0.6141	1.7483	-0.0631	0.2118	0.308	-0.2322	-0.2064	0.6984	-0.5335	-0.5648	0.279	0.2986	0.117	-0.0872	0.4045	-0.0406	0.4453	-25.1762	-9.8249	-46.7346
18	3.0559	-0.4338	-0.5493	1.3198	-0.9083	2.4685	-0.018	-0.1377	0.1289	0.096	0.0501	0.1052	-0.4324	-0.081	-0.0524	0.3591	0.0609	0.0287	0.1317	-0.0272	0.2102	-7.7103	2.3008	-21.0467
19	3.8894	-1.4306	-0.784	2.6006	-1.7323	3.8686	-0.1806	-0.5177	-0.2785	0.2043	0.2876	0.5431	-0.4859	-1.0167	-0.211	0.3605	0.1861	0.0961	0.3785	0.0641	0.3481	-19.4101	-0.6011	-14.0382
20	1.5274	-0.1195	0.0497	1.8373	-0.077	2.0986	0.0831	-0.0451	0.1492	0.1042	-0.0597	0.2273	-0.4101	-0.2546	-0.0064	0.3662	0.0715	0.0413	0.1872	0.002	0.2434	-11.8533	2.0337	-26.0779
21	1.7861	0.2139	1.2512	1.0088	0.6062	2.7427	-0.0287	-0.0481	-0.1522	0.0562	0.0287	0.0639	-0.1608	-0.095	-0.0317	0.2513	0.0483	0.0111	0.1936	0.0023	0.2195	-8.2147	-6.2935	-34.5972
22	3.5072	-1.0194	-0.5903	2.7826	-1.2823	4.111	-0.1207	0.0154	-0.1205	0.3211	0.1278	0.2348	-0.0968	-0.2823	-0.007	0.2369	0.0366	0.0318	0.1992	0.0075	0.2216	-7.968	-11.7527	-9.2091
23	5.4045	1.7495	-0.1685	6.7426	-1.7502	3.8341	0.0914	-0.8245	-0.3409	0.8577	-0.1488	0.2471	-0.9263	-0.4543	-0.1532	0.6357	0.1893	0.1986	0.4197	0.0244	0.3375	-16.9816	-5.7613	-2.6262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 46 )	A	1 - 46
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 57 )	A	47 - 57
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 58 through 72 )	A	58 - 72
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 73 through 94 )	A	73 - 94
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 117 )	A	95 - 117
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 118 through 136 )	A	118 - 136
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 137 through 157 )	A	137 - 157
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 27 )	B	1 - 27
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 36 )	B	28 - 36
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 37 through 46 )	B	37 - 46
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 47 through 57 )	B	47 - 57
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 72 )	B	58 - 72
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 73 through 94 )	B	73 - 94
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 95 through 117 )	B	95 - 117
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 118 through 126 )	B	118 - 126
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 127 through 136 )	B	127 - 136
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 137 through 157 )	B	137 - 157
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1 through 36 )	C	1 - 36
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 37 through 58 )	C	37 - 58
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 59 through 94 )	C	59 - 94
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 95 through 117 )	C	95 - 117
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 118 through 145 )	C	118 - 145
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 146 through 159 )	C	146 - 159

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