PDB-6ari: Crystal structure of a dephospho-CoA kinase from Escherichia coli...

ID or keywords:

Entry

Database: PDB / ID: 6ari

Title

Crystal structure of a dephospho-CoA kinase from Escherichia coli in complex with inhibitor CM078

Components

Dephospho-CoA kinase

Keywords

Transferase/Transferase Inhibitor / SSGCID / dephospho-CoA kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Transferase Inhibitor complex

Function / homology

Function and homology information

dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of a dephospho-CoA kinase from Escherichia coli in complex with inhibitor CM078
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.

History

Deposition	Aug 22, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 22, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ari.cif.gz	178.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ari.ent.gz	140.4 KB	Display	PDB format
PDBx/mmJSON format	6ari.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ari_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6ari_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6ari_validation.xml.gz	20.4 KB	Display
Data in CIF	6ari_validation.cif.gz	29.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ar/6ari ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6ari	HTTPS FTP

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Related structure data

Related structure data	4i1uS S: Starting model for refinement
Similar structure data	2h3c-d 5pyw-1 3o36-1 5py1-1 3o33-2 1uf9-3 5pxf-1 5pxd-1 5pxu-1 5pxi-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

Deposited unit

A: Dephospho-CoA kinase

B: Dephospho-CoA kinase

hetero molecules

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

1

A: Dephospho-CoA kinase

hetero molecules

defined by author&software
24.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dephospho-CoA kinase

hetero molecules

defined by author&software
24.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.720, 63.720, 221.080
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Dephospho-CoA kinase / Dephosphocoenzyme A kinase Mass: 23620.672 Da / Num. of mol.: 2 / Fragment: EscoA.00139.a.JV1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: coaE, yacE, b0103, JW0100 / Plasmid: EscoA.00139.a.JV1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6I9, dephospho-CoA kinase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-BQV / N-(methylsulfonyl)-3-{[(thiophen-2-yl)sulfanyl]methyl}benzamide Mass: 327.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₃NO₃S₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.75 Å³/Da / Density % sol: 55.2 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: JCSG_A3_Opt A11 (288528a11): 190 mM ammonium citrate dibasic, 21.23% (w/v) PEG3350: EscoA.00139.a.JV1 at 12mg/mL: bsi107694 10mM o/n soak: 20% eg: iku6-6

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 24, 2017

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 36249 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.477 % / B_iso Wilson estimate: 26.09 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.087 / R_rim(I) all: 0.092 / Χ²: 1.009 / Net I/σ(I): 16.49

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	8.615	0.591	3.95	2617	0.928	0.628	99.9
2.05-2.11	8.628	0.443	5.25	2556	0.952	0.47	100
2.11-2.17	8.623	0.357	6.36	2500	0.97	0.38	100
2.17-2.24	8.609	0.287	7.7	2408	0.979	0.305	100
2.24-2.31	8.598	0.245	8.75	2373	0.983	0.261	100
2.31-2.39	8.645	0.209	10.06	2265	0.989	0.222	100
2.39-2.48	8.597	0.176	11.69	2230	0.988	0.188	100
2.48-2.58	8.582	0.157	12.97	2131	0.99	0.167	100
2.58-2.7	8.579	0.134	14.73	2037	0.993	0.142	100
2.7-2.83	8.549	0.115	16.81	1964	0.994	0.122	100
2.83-2.98	8.532	0.095	19.93	1894	0.996	0.101	100
2.98-3.16	8.498	0.081	22.78	1759	0.997	0.086	99.9
3.16-3.38	8.427	0.07	26.13	1687	0.997	0.074	100
3.38-3.65	8.356	0.059	29.39	1566	0.998	0.063	100
3.65-4	8.307	0.053	31.97	1450	0.998	0.056	99.9
4-4.47	8.257	0.049	33.94	1316	0.998	0.053	100
4.47-5.16	8.157	0.047	35.6	1174	0.998	0.05	99.9
5.16-6.32	8.03	0.05	32.67	1028	0.998	0.054	99.8
6.32-8.94	7.759	0.045	34.42	808	0.999	0.048	100
8.94-44.171	6.726	0.04	35.19	486	0.998	0.044	98.8

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	(1.12rc0_2798: ???)	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4i1u

4i1u

Resolution: 2→44.171 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.92

	R_factor	Num. reflection	% reflection
R_free	0.2083	1948	5.38 %
R_work	0.1665	-	-
obs	0.1687	36241	99.95 %

Solvent computation

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

Displacement parameters

B_iso max: 87.17 Å² / B_iso mean: 33.625 Å² / B_iso min: 12.65 Å²

Refinement step

Cycle: final / Resolution: 2→44.171 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3002	0	118	305	3425
B_iso mean	-	-	60.87	41.38	-
Num. residues	-	-	-	-	403

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3214
X-RAY DIFFRACTION	f_angle_d	0.759	4401
X-RAY DIFFRACTION	f_chiral_restr	0.049	517
X-RAY DIFFRACTION	f_plane_restr	0.004	582
X-RAY DIFFRACTION	f_dihedral_angle_d	14.897	1910

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2-2.05	0.2679	112	0.1987	2406	2518
2.05-2.1054	0.2066	151	0.1739	2380	2531
2.1054-2.1674	0.2353	149	0.169	2401	2550
2.1674-2.2374	0.2197	146	0.1619	2374	2520
2.2374-2.3173	0.2262	133	0.1655	2440	2573
2.3173-2.4101	0.2083	128	0.1615	2429	2557
2.4101-2.5198	0.1918	136	0.1672	2439	2575
2.5198-2.6526	0.2503	132	0.1733	2443	2575
2.6526-2.8188	0.2556	137	0.1799	2413	2550
2.8188-3.0364	0.2727	147	0.176	2461	2608
3.0364-3.3418	0.2001	137	0.1752	2469	2606
3.3418-3.8252	0.1833	174	0.158	2422	2596
3.8252-4.8183	0.1805	140	0.1419	2530	2670
4.8183-44.1822	0.1834	126	0.1764	2686	2812

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	4.8073	0.6844	1.3228	4.1184	0.0857	4.8066	-0.1381	0.1187	0.3229	-0.0923	0.0009	0.1301	-0.1405	0.1242	0.1236	0.2231	0.0435	-0.0452	0.1683	0.0075	0.1711	-26.2891	2.9522	-32.907
2	2.5473	-2.5197	2.0658	2.6439	-1.7648	2.0346	0.0715	-0.4301	-0.1206	0.3806	-0.0468	0.1138	-0.1717	-0.4145	-0.1089	0.2432	-0.0138	-0.0106	0.2291	0.0203	0.1626	-33.858	8.5328	-42.3192
3	5.4194	-1.5813	-2.2092	2.6286	-1.2489	3.7254	-0.2645	0.4003	-0.6422	-0.0439	-0.0574	0.5206	0.5946	-0.4795	0.2899	0.2619	-0.0542	0.0205	0.2258	-0.0783	0.262	-45.6032	5.6882	-55.608
4	6.8908	3.6189	5.1459	5.093	2.8377	7.4956	-0.047	0.321	-0.1832	-0.0688	0.029	-0.2202	-0.0601	0.5245	0.031	0.1901	0.0661	0.0105	0.1892	0.025	0.1614	-30.4488	8.4116	-53.2631
5	2.5729	0.6834	0.1678	3.4184	-2.6038	4.0675	-0.2499	0.5366	-0.0208	-0.6168	0.187	0.1141	0.2121	0.2334	0.0719	0.2943	-0.003	-0.0365	0.2991	-0.0164	0.1859	-24.2663	-0.4514	-39.4251
6	2.3195	-0.1938	1.6054	7.698	0.7059	7.2957	0.3131	-0.4514	0.2853	0.0215	0.0757	0.874	0.1639	-1.0102	-0.3616	0.2564	-0.0159	-0.0393	0.3848	0.0285	0.3868	-41.5743	-9.4352	-30.7546
7	6.6942	2.3484	1.8894	3.6388	0.0516	2.9363	0.0392	0.3112	-0.6229	-0.498	0.1395	0.1973	0.6455	-0.2123	-0.1467	0.4616	-0.0001	-0.0956	0.2346	-0.0459	0.3155	-33.4299	-11.175	-36.2838
8	2.6752	2.8409	1.0533	5.7293	-0.2057	4.8884	-0.0846	-0.0654	-0.0611	0.1892	-0.0365	-0.3291	0.1662	0.393	0.2272	0.2566	0.0403	-0.0499	0.2961	-0.0074	0.2178	-17.2252	1.6004	-27.4959
9	2.1138	-0.275	-1.0789	2.3988	1.4096	4.3383	-0.1146	-0.0061	-0.3133	0.0529	-0.0941	0.4238	0.3064	-0.1489	0.1884	0.1684	-0.0583	-0.0099	0.1035	0.0071	0.1728	-27.0084	10.5498	-6.8288
10	1.7411	-0.5626	0.578	3.8448	-3.4479	3.1611	-0.1101	-0.125	-0.0807	0.1359	0.1082	-0.1622	-0.1511	-0.0526	0.0056	0.2046	-0.0375	-0.031	0.1623	-0.0246	0.1817	-24.8397	-4.3331	9.4937
11	3.782	3.6752	2.5993	3.6996	2.5127	2.3596	-0.29	-0.8231	1.0255	0.5361	-0.013	0.0703	-0.2896	-0.1913	0.2612	0.3953	-0.0385	-0.1274	0.3585	-0.1075	0.3341	-25.8047	-1.3231	21.7179
12	1.9759	-0.2583	2.3111	1.0894	-0.1776	8.2388	-0.0659	0.0561	0.1359	0.1037	-0.0118	-0.3051	-0.278	0.8134	0.0234	0.1963	-0.0784	-0.038	0.1927	0.0315	0.2769	-16.5874	-2.5407	7.15
13	1.7512	-1.9014	-1.8692	4.0838	1.3794	2.4619	-0.1444	-0.2985	0.1615	0.435	0.1857	-0.2456	0.2681	0.3718	-0.0095	0.2189	-0.0344	-0.0449	0.2058	-0.0094	0.1735	-20.0866	11.3224	-3.5328
14	4.2275	-0.8801	-3.7699	0.9425	0.1893	5.3068	-0.1385	-0.1278	-0.2072	0.0441	0.0951	-0.0622	0.1613	-0.0208	0.0289	0.162	-0.0395	-0.0089	0.1167	-0.0041	0.1358	-28.9055	22.0865	8.2425
15	2.8057	-1.8858	-1.3263	3.2755	2.4212	5.1026	0.0149	0.2145	-0.1062	-0.094	-0.0595	0.1638	-0.0024	0.0943	0.0222	0.1759	-0.0696	-0.0058	0.129	0.0113	0.1535	-23.5995	15.357	-14

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 27 )	A	1 - 27
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 40 )	A	28 - 40
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 41 through 77 )	A	41 - 77
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 78 through 102 )	A	78 - 102
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 103 through 133 )	A	103 - 133
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 134 through 145 )	A	134 - 145
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 146 through 178 )	A	146 - 178
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 179 through 200 )	A	179 - 200
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 27 )	B	1 - 27
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 28 through 54 )	B	28 - 54
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 55 through 77 )	B	55 - 77
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 78 through 102 )	B	78 - 102
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 103 through 133 )	B	103 - 133
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 134 through 168 )	B	134 - 168
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 169 through 203 )	B	169 - 203

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