PDB-5x6f: Crystal structure of Phosphopantetheine adenylyltransferase from ...

ID or keywords:

Entry

Database: PDB / ID: 5x6f

Title

Crystal structure of Phosphopantetheine adenylyltransferase from Pseudomonas aeruginosa

Components

Phosphopantetheine adenylyltransferase

Keywords

TRANSFERASE / Phosphopantetheine adenylyltransferase / Pseudomonas aeruginosa

Function / homology

Function and homology information

[citrate (pro-3S)-lyase] ligase activity / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 2.593 Å

Authors

Mondal, A. / Chatterjee, R. / Datta, S.

Funding support

India, 2items

Citation

Journal: J Phys Chem B / Year: 2018
Title: Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase Allosteric Cleft.
Authors: Mondal, A. / Chatterjee, R. / Datta, S.

History

Deposition	Feb 21, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5x6f.cif.gz	379 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5x6f_validation.pdf.gz	503.6 KB	Display	wwPDB validaton report
Full document	5x6f_full_validation.pdf.gz	524.7 KB	Display
Data in XML	5x6f_validation.xml.gz	34.3 KB	Display
Data in CIF	5x6f_validation.cif.gz	45.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6f ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6f	HTTPS FTP

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Related structure data

Similar structure data	3x1k-d 1b6t-1 6cho-1 6b7b-1 6b7f-1 1vlh-d 6b7e-1 6chl-1 1qjc-1 6b7d-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Phosphopantetheine adenylyltransferase

B: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

D: Phosphopantetheine adenylyltransferase

E: Phosphopantetheine adenylyltransferase

F: Phosphopantetheine adenylyltransferase

hetero molecules

107 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

E: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase

C: Phosphopantetheine adenylyltransferase

E: Phosphopantetheine adenylyltransferase

defined by author&software
107 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphopantetheine adenylyltransferase

D: Phosphopantetheine adenylyltransferase

F: Phosphopantetheine adenylyltransferase

hetero molecules

B: Phosphopantetheine adenylyltransferase

D: Phosphopantetheine adenylyltransferase

F: Phosphopantetheine adenylyltransferase

hetero molecules

defined by author&software
108 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.691, 65.035, 124.984
Angle α, β, γ (deg.)	90.00, 101.25, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT Mass: 17795.473 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: coaD, PA0363 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I6D1, pantetheine-phosphate adenylyltransferase
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.53 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 7 Details: PEG 4000, 0.1M HEPES pH 7.0, 5% isopropanol, 200mM sodium acetate

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Data collection

Diffraction	Mean temperature: 98.15 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 15, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.59→32.39 Å / Num. obs: 29671 / % possible obs: 95 % / Redundancy: 3.1 % / Net I/σ(I): 16.14

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155)	refinement
HKL-2000		data scaling

Refinement

Resolution: 2.593→32.388 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / Phase error: 34.18

	R_factor	Num. reflection	% reflection
R_free	0.2906	1993	7.53 %
R_work	0.2654	-	-
obs	0.2673	26454	95.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.593→32.388 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7464	0	38	23	7525

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7657
X-RAY DIFFRACTION	f_angle_d	0.583	10351
X-RAY DIFFRACTION	f_dihedral_angle_d	15.329	4630
X-RAY DIFFRACTION	f_chiral_restr	0.043	1176
X-RAY DIFFRACTION	f_plane_restr	0.004	1338

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 (%)
2.5931-2.6579	0.3584	119	0.3559	1455	X-RAY DIFFRACTION	80
2.6579-2.7298	0.3446	142	0.333	1739	X-RAY DIFFRACTION	95
2.7298-2.81	0.3388	146	0.3346	1787	X-RAY DIFFRACTION	98
2.81-2.9007	0.3538	143	0.311	1759	X-RAY DIFFRACTION	98
2.9007-3.0043	0.3629	147	0.3028	1796	X-RAY DIFFRACTION	98
3.0043-3.1245	0.341	146	0.3073	1815	X-RAY DIFFRACTION	98
3.1245-3.2666	0.322	145	0.3035	1783	X-RAY DIFFRACTION	98
3.2666-3.4386	0.3334	145	0.2971	1777	X-RAY DIFFRACTION	98
3.4386-3.6538	0.3148	131	0.3078	1608	X-RAY DIFFRACTION	89
3.6538-3.9354	0.2987	134	0.2759	1667	X-RAY DIFFRACTION	92
3.9354-4.3306	0.2766	148	0.2335	1795	X-RAY DIFFRACTION	96
4.3306-4.9554	0.2208	145	0.221	1774	X-RAY DIFFRACTION	97
4.9554-6.2359	0.293	149	0.2347	1846	X-RAY DIFFRACTION	99
6.2359-32.3903	0.2275	153	0.2093	1860	X-RAY DIFFRACTION	98

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	3.9368	1.1302	0.3294	3.777	-1.4761	0.7405	0.7637	0.7185	-0.1119	0.7115	0.3749	0.3093	-0.4519	-0.0506	-1.0719	0.9735	0.2746	-0.0252	1.5393	-0.1966	0.5314	-5.0233	-32.7702	-48.1848
2	0.167	-0.561	-0.0765	2.4273	0.3559	0.0517	-0.2513	0.0882	-0.3247	-0.3765	-0.0943	0.2436	0.456	0.2231	0.4285	0.9624	0.0569	0.2753	1.4874	-0.0817	0.5246	-5.1375	-27.9763	-53.0423
3	0.3803	0.3504	0.4867	0.4981	-0.1489	2.5651	-0.0626	-0.0661	0.0154	-0.21	0.1933	0.0466	0.087	-0.2465	-0.0007	0.8778	0.1623	0.1255	1.355	0.0879	0.4021	-3.1033	-30.4946	-40.468
4	3.9843	-3.2914	-1.5834	4.3441	1.2077	4.2485	-0.258	0.6354	0.7279	0.5101	-0.1314	-0.5932	0.4873	0.4264	0.3218	0.7895	-0.1499	-0.061	1.3179	0.0521	0.7106	-7.0821	-39.2226	-50.3706
5	8.5334	-3.9952	5.1631	8.9149	0.4537	6.3325	-0.7168	1.3438	-0.0382	0.2744	-1.0565	-0.2683	0.8719	-0.215	1.7584	1.3477	0.2242	0.2169	1.2498	-0.0241	0.6454	-2.7099	-47.9577	-53.6055
6	2.1741	1.0475	-1.0689	0.7648	-0.7781	0.7888	-0.5474	0.9782	-0.0053	0.2317	0.4139	0.0224	0.3527	0.2096	0.1402	0.8789	0.1744	0.0713	1.3742	0.1181	0.6656	6.8391	-31.2293	-50.5326
7	2.0896	0.4278	0.2869	0.1857	-0.1171	0.3514	-0.9698	0.3538	0.542	-0.1156	0.519	0.1376	-0.0804	0.0212	0.4351	1.4634	0.0533	-0.3689	1.0926	-0.1117	0.5983	10.3574	-22.9277	-36.4766
8	1.2936	0.2305	-0.453	2.1243	-0.2308	0.5562	-0.0039	0.1476	0.0028	0.035	0.1655	0.0472	0.0281	-0.0935	0.0058	0.2531	-0.054	-0.2546	0.1462	0.0008	0.9381	15.263	-28.554	-15.1855
9	0.0281	0.0082	0.1033	1.0394	0.3358	0.4973	-0.0717	-0.1182	0.0893	0.0937	-0.0912	0.4213	0.0575	-0.2986	-0.0354	0.1838	-0.1974	-0.2484	0.1044	-0.0968	1.3068	18.194	-36.5948	-11.5794
10	7.7329	-4.8048	0.532	3.9385	-0.7521	1.2848	-0.5103	-0.5934	0.2468	-0.0846	0.7731	-0.0158	-0.1234	-0.1797	-0.1751	0.2624	-0.0283	-0.0771	0.2999	0.0233	1.1812	12.0595	-32.6146	-4.4478
11	1.1326	-0.1288	-0.4049	1.6779	0.4572	0.5933	0.0999	0.304	0.5109	-0.4796	-0.4524	-0.1017	-0.1133	0.0331	0.1869	0.3013	0.1559	-0.1213	0.2083	0.0039	0.9195	-0.2521	-23.5873	-20.505
12	7.3087	-0.6618	1.3915	2.9918	4.7465	8.3655	-1.1506	-0.9322	0.4996	1.1438	0.6264	1.1425	1.6621	-0.0591	0.531	0.9607	-0.0686	0.2334	1.281	-0.0047	0.7951	-8.8011	-39.107	-74.4993
13	2.4089	0.6601	1.5623	2.6148	1.6363	1.6462	-0.4594	0.3279	0.2485	0.0722	-0.2588	0.2187	0.1121	-0.5006	0.7165	1.0621	-0.0258	-0.0673	1.527	-0.0888	0.454	-9.735	-42.9432	-77.5626
14	1.8752	0.813	-0.4644	2.4754	1.155	1.0038	-0.3987	0.7461	-0.1569	-0.5641	0.0806	0.3254	0.4411	-0.4195	0.3964	0.9967	-0.1041	0.0127	1.5233	-0.1072	0.6217	-7.9936	-35.7249	-74.6528
15	6.2991	-3.4328	-3.7732	8.6556	2.7399	2.3329	-1.5863	-0.9956	0.3692	1.5149	0.6233	-0.7382	-0.0688	0.703	0.9941	0.9608	-0.0136	-0.2027	1.6238	0.1642	0.6422	5.9827	-33.5461	-69.0339
16	2.3383	-3.9591	-2.3538	9.6128	4.1471	2.3781	0.5778	0.603	2.0611	-1.284	-0.2601	-0.513	0.484	-0.9635	-0.3607	1.3132	0.2106	0.0138	1.1767	0.1347	1.3888	-3.3406	-30.821	-66.1089
17	3.2374	-0.9214	-2.2989	3.8678	2.8406	2.9586	-0.9999	-2.4482	-1.0273	0.8951	-0.4976	-0.5515	-0.1654	2.1001	1.4823	1.592	0.5868	0.1028	1.9606	0.5037	1.0244	-5.1734	-52.9907	-65.8321
18	6.5905	-4.5941	-4.1165	4.7608	3.1553	5.1518	-0.94	-0.2018	-0.8719	0.9114	-0.1078	0.3848	0.151	0.5613	1.0457	0.9982	-0.1158	0.1104	1.11	0.0476	0.7552	-5.9079	-57.6088	-82.1578
19	2.4776	-1.1506	0.2765	0.5764	0.0516	0.8051	-0.0695	0.0686	0.3684	-0.0278	-0.1522	-0.3109	-0.1038	0.1246	0.1023	0.2388	0.0146	-0.1667	0.1818	0.0773	0.8959	20.9858	-36.9919	13.1721
20	1.9585	0.5143	0.4438	1.0043	0.0195	1.435	0.1906	-0.091	0.153	0.0143	0.0078	0.1175	0.0484	0.0109	-0.2276	0.1726	-0.0374	-0.1767	0.2303	0.0352	0.9651	22.0992	-40.817	16.128
21	1.3223	-1.0658	-0.8136	0.8746	0.5971	0.9209	-0.0087	-0.2356	-0.1437	-0.2023	-0.0792	-0.1885	-0.23	0.1795	0.0758	0.2849	-0.0695	-0.1275	0.2111	0.0442	0.9403	22.8882	-31.83	16.886
22	0.4892	-0.38	-0.2349	0.299	0.1913	0.1105	0.0008	0.1057	-0.7685	-0.1685	-0.0967	0.3543	0.1522	-0.1625	-0.1008	0.3715	-0.0307	-0.2221	0.2603	-0.0403	1.4387	10.7218	-33.4364	7.9475
23	0.4363	0.532	-0.5038	7.7567	-0.3922	0.8851	-0.0242	-0.3834	-0.5625	-0.5608	0.1965	-0.9124	0.3033	0.0789	-0.1436	0.2267	-0.066	-0.2496	0.2906	-0.0234	0.7647	16.4873	-40.3902	4.5289
24	1.8517	-0.9685	0.3617	1.9908	0.4751	0.8155	-0.1304	-0.2454	-0.6915	0.2614	-0.0447	-0.1056	-0.0864	-0.125	0.0035	0.2892	0.0976	-0.1857	0.1444	0.0758	0.8672	18.0702	-55.5415	20.7993
25	2.685	-0.4277	1.2927	1.632	1.7544	4.1829	0.105	0.869	-0.3076	-2.3044	-0.0483	-0.1223	-0.2567	0.0342	-0.0337	1.6262	-0.2675	0.1614	0.9542	-0.0699	0.6329	8.4097	-68.8709	-48.2499
26	2.4616	-0.7003	-0.0403	6.2602	4.7654	3.7813	0.2213	-0.0104	0.0111	0.7897	0.3023	-0.0188	0.1733	-0.4633	-0.4297	0.9729	0.0518	0.16	1.1509	0.1517	0.6544	4.5471	-67.8415	-45.32
27	2.1188	0.2857	1.015	1.7518	0.241	0.4917	-0.1957	0.1507	0.2844	-0.1025	-0.285	0.2778	0.4447	0.6549	0.4952	1.1333	-0.0458	0.1575	1.3893	-0.0096	0.4445	14.4985	-66.4694	-49.7574
28	6.0329	-2.2044	-0.4533	3.952	3.7727	4.1671	-0.2963	-0.6692	-0.6938	-0.5815	0.1581	-0.3518	-1.0798	1.1425	0.058	0.979	0.0715	0.2964	1.8301	0.1878	0.7474	18.2903	-68.1457	-56.3686
29	7.0938	1.0838	-3.1968	9.049	4.3055	4.029	0.0476	0.1737	-0.2015	-1.8773	-1.4146	1.0671	-1.7323	-0.4135	1.2892	1.2125	0.4045	-0.1343	1.5185	0.1643	0.678	-1.5411	-58.9585	-57.0793
30	7.2719	0.1928	0.4279	9.8673	0.3083	0.0352	0.1252	1.3039	-0.12	1.1606	0.0572	0.6587	-0.3135	0.1442	-0.155	1.0244	0.1223	0.0712	1.4117	0.0941	0.5576	-6.3543	-57.1693	-40.7196
31	1.3889	-0.2798	0.1732	3.4188	0.3831	1.9304	-0.0227	-0.0639	-0.2911	-0.0853	0.2763	-0.1757	-0.1083	0.0524	-0.147	0.2183	0.0376	-0.0977	0.1032	-0.0004	0.7419	6.6536	-66.0829	-15.2754
32	2.0612	0.0897	-0.7158	0.2375	-0.445	0.9423	-0.0118	-0.354	0.4155	-0.0271	0.0041	-0.0355	-0.2169	0.1691	0.046	0.1829	0.0436	-0.2412	0.1809	-0.0249	1.0438	-2.7215	-64.6452	-10.4442
33	1.6348	-0.1288	-0.3131	1.2025	-0.7109	1.6861	-0.2574	-0.0993	-0.1169	0.2089	-0.0979	-0.0651	-0.2018	0.2615	0.2244	0.2051	-0.0365	-0.1056	0.263	-0.0536	0.9643	17.3114	-55.6396	-16.3919

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 36 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 37 through 72 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 73 through 94 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 108 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 109 through 146 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 147 through 158 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 56 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 57 through 108 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 109 through 127 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 128 through 158 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 14 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 15 through 57 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 58 through 94 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 95 through 108 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 109 through 117 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 118 through 127 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 128 through 158 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 14 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 15 through 58 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 59 through 79 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 80 through 108 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 109 through 127 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 128 through 158 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 1 through 14 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 15 through 57 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 58 through 108 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 109 through 117 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 118 through 127 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 128 through 158 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 1 through 57 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 58 through 117 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 118 through 158 )

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