PDB-7ab5: Crystal structure of the Escherichia coli toxin-antitoxin system ...

ID or keywords:

Entry

Database: PDB / ID: 7ab5

Title

Crystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT D233Q)

Components

Couple_hipA domain-containing protein
HipA_C domain-containing protein
Predicted transcriptional regulator, XRE family

Keywords

TOXIN / antitoxin / kinase / HTH / HipA / HipT / HipB / HipS / HipBA / HipBST / bacteria / TrpS / phosphorylation / trans-autophosphorylation

Function / homology

Function and homology information

protein serine/threonine kinase activity / DNA binding / cytosol
Similarity search - Function

Biological species

Escherichia coli O127:H6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.9 Å

Authors

Baerentsen, R.L. / Brodersen, D.E.

Funding support

Denmark, 2items

Citation

Journal: Biorxiv / Year: 2022
Title: Structural basis for regulation of a tripartite toxin-antitoxin system by dual phosphorylation
Authors: Baerentsen, R.L. / Nielsen, S.V. / Lyngso, J. / Bisiak, F. / Pedersen, J.S. / Gerdes, K. / Sorensen, M.A. / Brodersen, D.E.

History

Deposition	Sep 6, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	May 1, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model Item: _citation.journal_id_ISSN

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ab5.cif.gz	428.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ab5_validation.pdf.gz	474.2 KB	Display	wwPDB validaton report
Full document	7ab5_full_validation.pdf.gz	491.3 KB	Display
Data in XML	7ab5_validation.xml.gz	35.9 KB	Display
Data in CIF	7ab5_validation.cif.gz	48.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/7ab5 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/7ab5	HTTPS FTP

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Related structure data

Related structure data	7ab3C 7ab4C C: citing same article (ref.)
Similar structure data	7ab4-d 1q0g-d 3gnv-d 1q0d-d 4p12-d 2dfu-d 1i7r-d 1i1f-d 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	#144 - Dec 2011 Complex I similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: Predicted transcriptional regulator, XRE family

B: Couple_hipA domain-containing protein

C: HipA_C domain-containing protein

D: Predicted transcriptional regulator, XRE family

E: Couple_hipA domain-containing protein

F: HipA_C domain-containing protein

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

1

Idetical with deposited unit
defined by author
Evidence: SAXS

Unit cell

Length a, b, c (Å)	281.661, 106.467, 57.753
Angle α, β, γ (deg.)	90.000, 90.750, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Predicted transcriptional regulator, XRE family Mass: 11720.580 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC / Gene: E2348C_3787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL98
#2: Protein	Couple_hipA domain-containing protein Mass: 11713.165 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC / Gene: E2348C_3786 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL97
#3: Protein	HipA_C domain-containing protein Mass: 39082.141 Da / Num. of mol.: 2 / Mutation: D233Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC / Gene: E2348C_3785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL96
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.47 Å³/Da / Density % sol: 64.63 % / Description: Plate
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M BICINE, 6% MPD

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

MAX IV

/ Beamline: BioMAX / Wavelength: 1.5418 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019

Radiation

Monochromator: At 26 m, Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.9→49.86 Å / Num. obs: 73090 / % possible obs: 98.7 % / Redundancy: 3.332 % / B_iso Wilson estimate: 77.87 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.187 / R_rim(I) all: 0.223 / Χ²: 0.955 / Net I/σ(I): 4.76 / Num. measured all: 243549 / Scaling rejects: 4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.9-2.98	3.317	1.404	0.62	17686	5450	5332	0.188	1.681	97.8
2.98-3.06	3.354	1.142	0.84	17750	5345	5292	0.274	1.365	99
3.06-3.15	3.36	0.969	1.05	17289	5183	5146	0.362	1.159	99.3
3.15-3.25	3.359	0.77	1.42	16687	5035	4968	0.497	0.921	98.7
3.25-3.35	3.34	0.649	1.71	16322	4940	4887	0.611	0.777	98.9
3.35-3.47	3.296	0.519	2.22	15249	4684	4626	0.696	0.623	98.8
3.47-3.6	3.297	0.419	2.72	14953	4608	4535	0.797	0.503	98.4
3.6-3.75	3.278	0.355	3.27	14136	4363	4313	0.842	0.426	98.9
3.75-3.92	3.315	0.256	4.34	13824	4238	4170	0.919	0.307	98.4
3.92-4.11	3.298	0.2	5.31	13107	4012	3974	0.952	0.239	99.1
4.11-4.33	3.259	0.166	6.41	12281	3809	3768	0.96	0.199	98.9
4.33-4.59	3.242	0.14	7.54	11611	3613	3581	0.97	0.168	99.1
4.59-4.91	3.4	0.117	8.97	11438	3400	3364	0.981	0.139	98.9
4.91-5.3	3.432	0.124	8.69	10858	3190	3164	0.978	0.147	99.2
5.3-5.81	3.412	0.126	8.59	9870	2928	2893	0.977	0.15	98.8
5.81-6.49	3.386	0.126	8.62	8738	2614	2581	0.975	0.15	98.7
6.49-7.5	3.341	0.109	9.56	7540	2300	2257	0.979	0.13	98.1
7.5-9.18	3.38	0.077	13.03	6560	1970	1941	0.99	0.092	98.5
9.18-12.99	3.411	0.053	17.3	5075	1502	1488	0.995	0.063	99.1
12.99-49.86	3.179	0.05	18.19	2575	843	810	0.994	0.061	96.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.9 Å	70.41 Å
Translation	2.9 Å	70.41 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc5_4047	refinement
XDS	VERSION Mar 15, 2019 BUILT=20190315	data reduction
XSCALE	VERSION Mar 15, 2019 BUILT=20190315	data scaling
PHASER	2.8.2	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PBD-code from depostion entry D_1292109701

Resolution: 2.9→49.86 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2263	1913	5.07 %	RANDOM
R_work	0.193	35784	-	-
obs	0.1947	37697	99.83 %	-

Solvent computation

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

Displacement parameters

B_iso max: 271 Å² / B_iso mean: 89.9688 Å² / B_iso min: 37.63 Å²

Refinement step

Cycle: final / Resolution: 2.9→49.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8178	0	0	5	8183
B_iso mean	-	-	-	59.26	-
Num. residues	-	-	-	-	1015

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.9-2.98	0.3331	119	0.3212	2513	2632	99
2.98-3.06	0.3457	144	0.3085	2552	2696	100
3.06-3.15	0.365	164	0.3012	2490	2654	100
3.15-3.25	0.3399	132	0.2944	2568	2700	100
3.25-3.37	0.3082	141	0.2832	2546	2687	100
3.37-3.5	0.3261	134	0.2548	2547	2681	100
3.5-3.66	0.3122	145	0.222	2537	2682	100
3.66-3.85	0.2393	134	0.1993	2578	2712	100
3.85-4.09	0.2599	116	0.1829	2566	2682	100
4.09-4.41	0.171	148	0.1611	2537	2685	100
4.41-4.85	0.1708	138	0.1423	2576	2714	100
4.85-5.55	0.1639	144	0.1491	2543	2687	100
5.55-6.99	0.2136	105	0.1852	2618	2723	100
7-49.86	0.1849	149	0.1581	2613	2762	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	8.0659	-4.9516	4.7247	4.7035	-4.6289	4.5453	-0.1106	0.3068	0.0467	-0.3291	-0.603	-1.307	0.3578	1.129	0.4085	0.7284	0.0911	0.1647	0.6268	0.0083	1.0295	94.6978	-27.3178	9.1228
2	5.8697	3.9003	1.0259	3.6023	3.3158	7.5051	-0.763	0.6152	-0.5574	-1.6616	1.2079	-1.356	0.3112	0.1977	-0.3622	0.5841	-0.0484	0.1125	0.551	-0.029	0.5976	85.5363	-32.6641	4.1779
3	5.5985	2.9364	-2.6612	4.1372	-1.0811	6.9114	-0.0411	0.629	0.1445	-0.3481	0.2872	0.7613	-0.3521	-0.097	0.0405	0.5523	-0.0746	-0.0452	0.5901	-0.0727	0.5852	72.043	-37.4183	7.6549
4	3.1371	2.2386	-3.6068	8.4909	-2.0699	7.1128	0.4469	1.188	2.166	-0.8408	0.3546	0.8775	-0.6592	-0.9135	-0.8046	0.6645	0.0559	-0.0717	0.564	0.127	0.7148	75.2169	-27.5067	3.6043
5	6.8865	3.87	0.6702	2.4792	-1.0465	6.3065	0.1833	0.2174	0.6593	0.1431	-0.5395	0.4854	-0.7204	-0.0311	0.3159	0.542	0.0226	0.0734	0.4962	0.0392	0.6065	79.4738	-25.6332	11.8924
6	9.7465	3.061	2.216	7.8475	1.6951	7.9552	-0.5572	-0.063	-1.0624	0.9296	0.6729	-0.8023	0.39	1.0945	-0.0361	0.5115	0.0538	-0.0775	0.5707	-0.0332	0.5485	90.2846	-29.0849	16.8098
7	4.2145	-2.6244	-0.5314	4.1676	0.6554	7.1558	-0.0007	-1.133	-0.0324	0.8812	0.5046	-1.4687	0.695	1.7845	-0.5087	0.8711	0.1249	-0.3366	1.9752	-0.1086	1.3177	106.2737	-59.3261	31.4706
8	8.2406	-1.9998	-0.4142	5.6833	-3.4954	7.6866	0.6559	-1.5334	-0.3298	1.3265	0.5327	-0.7075	-0.3866	1.8244	-0.9992	0.8438	0.0109	-0.2097	1.2604	-0.287	0.9475	97.7862	-55.6578	31.9213
9	4.0951	3.2965	-0.0412	5.0524	4.6837	9.3174	0.0963	-0.6628	-0.7349	0.4752	-0.5905	-0.1333	1.0111	1.0649	0.5044	1.7884	0.257	-0.5525	1.4017	0.1017	1.3403	90.6947	-76.6458	24.0275
10	6.9566	0.1698	3.4169	2.7226	3.4349	5.8024	1.5205	0.0161	-0.3165	0.6222	-0.3242	0.621	0.4883	0.4869	-1.4206	2.7688	0.4383	-0.168	2.0792	0.5218	2.3698	96.3857	-78.1491	32.9541
11	4.523	-3.8628	3.114	5.3989	-2.8893	2.1683	0.3344	-0.7464	0.0826	0.3314	-0.3894	0.3473	1.1887	1.9358	0.2377	0.9778	0.2647	-0.2446	1.3587	-0.007	1.0251	102.1807	-67.9994	24.0776
12	6.6457	-1.2359	1.072	5.23	0.3082	5.3284	0.2716	0.3543	-0.4302	-0.2413	-0.0064	-0.406	0.5943	0.6427	-0.2499	0.5575	0.0851	-0.0046	0.4166	-0.1348	0.6409	86.7307	-74.5071	3.909
13	2.2522	-0.7026	-0.3426	3.4867	1.6448	3.5268	-0.0468	0.0238	-0.1413	0.2397	0.0016	0.0426	0.3618	-0.0216	0.0619	0.4928	-0.0321	-0.04	0.3836	0.0244	0.3807	74.8045	-60.5847	16.6167
14	8.318	-2.7681	1.6589	2.474	1.2218	2.3677	-0.2085	-0.8603	-0.2924	1.7754	0.3716	-0.2099	0.7904	0.4122	-0.776	0.7434	-0.0672	-0.1472	0.748	0.0483	0.6905	90.7548	-27.6115	22.7392
15	5.9937	5.7581	3.0148	8.4132	1.8371	9.6253	1.0862	-0.9232	-0.2416	1.9857	-0.6422	-0.3207	-0.3066	-0.0397	-0.41	0.7011	-0.0273	0.0144	0.4629	-0.003	0.5714	88.9863	-16.1603	24.6459
16	8.8311	4.076	1.262	6.3212	0.0961	7.0619	0.0073	0.8035	1.6915	-0.0091	-0.3516	0.3861	-1.2468	-0.6962	0.249	0.7752	0.0442	0.1423	0.5774	0.1546	0.6693	88.255	-3.6009	16.9193
17	7.1268	3.5626	-2.9781	9.4783	-6.6265	4.7084	0.0022	-0.108	-0.3041	0.6046	0.9294	1.6838	-0.4105	-1.2313	-0.6461	0.7196	0.0896	0.07	0.574	0.0068	0.8234	79.9882	-10.8795	19.7029
18	6.5566	4.7118	0.8328	6.2479	2.7902	6.5543	-0.1609	0.4218	0.484	-0.4173	0.1764	0.269	0.3037	0.3646	0.0669	0.7178	0.0638	0.1446	0.4236	0.0691	0.7505	83.7909	-16.9422	13.7549
19	6.338	3.3688	1.2157	3.4725	4.568	9.4377	-0.0024	1.1706	-0.5519	0.2139	0.5022	-2.2042	0.6736	0.4638	-0.3802	0.5592	0.0883	0.1027	0.6042	-0.01	0.7068	93.4123	-24.742	14.852
20	3.3619	0.014	-0.1691	6.1118	3.5369	9.9409	-0.132	0.2491	-1.2764	0.3179	0.2149	-1.5887	0.9925	1.688	0.1267	0.8858	0.2433	0.1589	0.8985	-0.0407	1.4509	131.6722	-22.8614	15.4381
21	2.6128	4.1071	-0.3844	7.7586	-1.3078	2.5482	-0.145	-0.2109	-0.8724	-0.1047	-0.0307	-0.7951	1.177	0.6894	0.2249	0.8976	0.1359	0.01	0.8342	-0.0609	1.2588	123.9825	-20.6513	13.0734
22	7.7129	4.5261	2.5344	7.3742	4.2077	7.0506	-0.1735	0.0824	-2.6138	-0.9367	-0.0144	-1.6576	0.6542	0.3412	0.1111	0.8322	0.1269	0.0566	0.8974	-0.075	1.3869	137.8846	-0.2299	19.6401
23	3.1206	0.3882	4.8828	7.9557	2.7529	8.2781	-0.7535	0.3648	-0.3671	-1.4826	-0.4763	-1.7967	-2.7595	2.6648	0.9674	1.3227	-0.2424	-0.0032	1.4305	-0.2932	1.7603	139.1991	-10.0556	14.083
24	6.4008	6.7954	1.7167	7.7937	-0.2736	7.9364	0.0568	-1.0689	-0.3643	0.6021	-0.2576	-0.0869	0.6908	0.5508	-0.208	0.7226	0.2108	-0.1043	0.833	-0.0744	0.9796	130.5738	-16.0757	23.7995
25	5.0837	-1.1483	0.0397	6.0119	0.946	4.0147	0.1217	-0.3674	-0.2024	0.0771	-0.1717	-0.1197	-0.2214	0.4025	-0.0222	0.5358	-0.069	-0.0537	0.6511	-0.0057	0.4337	122.8579	7.6905	33.7082
26	3.111	0.2111	1.2773	1.5363	0.2775	1.9539	0.0312	0.2003	-0.0922	-0.21	-0.0547	-0.1145	0.0676	0.2118	0.043	0.6337	0.0135	0.1547	0.4962	0.0121	0.4976	112.1503	3.3176	14.7726
27	3.8771	-0.2444	6.023	4.8493	0.3402	9.8417	-0.2546	-0.0389	0.4181	-0.4762	-0.1168	0.2644	-0.7787	0.0692	0.4441	0.7149	0.0348	0.091	0.6166	-0.0463	0.6238	107.3199	18.4517	14.5792

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 38 through 44 )	A	38 - 44
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 59 )	A	45 - 59
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 60 through 70 )	A	60 - 70
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 71 through 83 )	A	71 - 83
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 98 )	A	84 - 98
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 99 through 107 )	A	99 - 107
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 33 )	B	2 - 33
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 60 )	B	34 - 60
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 61 through 71 )	B	61 - 71
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 72 through 82 )	B	72 - 82
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 83 through 101 )	B	83 - 101
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 86 )	C	2 - 86
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 87 through 338 )	C	87 - 338
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 38 through 44 )	D	38 - 44
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 45 through 59 )	D	45 - 59
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 60 through 70 )	D	60 - 70
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 71 through 83 )	D	71 - 83
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 84 through 98 )	D	84 - 98
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 99 through 107 )	D	99 - 107
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 2 through 28 )	E	2 - 28
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 29 through 63 )	E	29 - 63
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 64 through 74 )	E	64 - 74
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 75 through 89 )	E	75 - 89
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 90 through 101 )	E	90 - 101
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 2 through 86 )	F	2 - 86
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 87 through 312 )	F	87 - 312
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 313 through 341 )	F	313 - 341

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