PDB-6g1c: Crystal structure of the N-terminal domain of Burkholderia Pseudo...

ID or keywords:

Entry

Database: PDB / ID: 6g1c

Title

Crystal structure of the N-terminal domain of Burkholderia Pseudomallei antitoxin HicB

Components

Antitoxin HicB

Keywords

ANTITOXIN / N-terminal domain of the antitoxin HicB which acts as an inhibitor to HicA

Function / homology

HicB-like antitoxin of toxin-antitoxin system / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like / HicB-like antitoxin of toxin-antitoxin system domain-containing protein

Function and homology information

Biological species

Burkholderia pseudomallei K96243 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Winter, A.J. / Williams, C. / Crump, M.P.

Funding support

United Kingdom, 1items

Citation

Journal: J Biol Chem / Year: 2018
Title: The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.
Authors: Ashley J Winter / Christopher Williams / Michail N Isupov / Hannah Crocker / Mariya Gromova / Philip Marsh / Oliver J Wilkinson / Mark S Dillingham / Nicholas J Harmer / Richard W Titball / Matthew P Crump /

Abstract: Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which ...

History

Deposition	Mar 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2018	Group: Data collection / Database references / Structure summary Category: citation / entity Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description
Revision 1.2	May 8, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6g1c.cif.gz	145.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6g1c.ent.gz	116.2 KB	Display	PDB format
PDBx/mmJSON format	6g1c.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/g1/6g1c ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1c	HTTPS FTP

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Related structure data

Related structure data	SASDD45C SASDD55C 6g1nC 6g26C C: citing same article (ref.)
Similar structure data	2giz-1 4yew-d 2n6d-d 2zdp-d 2giz-2 6ryl-2 2zdo-2 1lpd-d 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

V: Antitoxin HicB

A: Antitoxin HicB

B: Antitoxin HicB

C: Antitoxin HicB

40.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

V: Antitoxin HicB

C: Antitoxin HicB

defined by author&software
Evidence: gel filtration, Gel filtration resulted in a dimer, mass spectrometry, Native mass spectrometry showed existance of a dimer state in the gas phase
20.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Antitoxin HicB

B: Antitoxin HicB

defined by author&software
20.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.447, 76.685, 76.907
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Antitoxin HicB Mass: 10147.295 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria) Gene: BPSS0391 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63NA5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M NaOAc, 8% (w/v) PEG 4000, 15% (v/v) MPD

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.56→54.303 Å / Num. obs: 54080 / % possible obs: 100 % / Redundancy: 13.2 % / B_iso Wilson estimate: 36.69 Å² / CC_1/2: 1 / R_merge(I) obs: 0.03715 / R_rim(I) all: 0.03872 / Net I/σ(I): 29.88
Reflection shell	Resolution: 1.56→1.616 Å / Redundancy: 13 % / R_merge(I) obs: 1.209 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 5244 / CC_1/2: 0.845 / R_rim(I) all: 1.259 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.56→54.303 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2329	2773	5.15 %	RANDOM
R_work	0.1995	-	-	-
obs	0.2013	53829	99.48 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.56→54.303 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2502	0	0	267	2769

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	2554
X-RAY DIFFRACTION	f_angle_d	1.141	3493
X-RAY DIFFRACTION	f_dihedral_angle_d	16.528	1489
X-RAY DIFFRACTION	f_chiral_restr	0.08	421
X-RAY DIFFRACTION	f_plane_restr	0.009	443

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 (%)
1.5598-1.5867	0.4967	134	0.4181	2416	X-RAY DIFFRACTION	96
1.5867-1.6156	0.4157	154	0.3785	2460	X-RAY DIFFRACTION	98
1.6156-1.6466	0.3851	129	0.3452	2508	X-RAY DIFFRACTION	99
1.6466-1.6802	0.3808	135	0.3236	2531	X-RAY DIFFRACTION	99
1.6802-1.7168	0.3542	127	0.3079	2520	X-RAY DIFFRACTION	99
1.7168-1.7567	0.308	147	0.2847	2520	X-RAY DIFFRACTION	99
1.7567-1.8007	0.3139	127	0.2693	2517	X-RAY DIFFRACTION	100
1.8007-1.8493	0.2952	118	0.2489	2577	X-RAY DIFFRACTION	100
1.8493-1.9038	0.2948	111	0.2261	2567	X-RAY DIFFRACTION	100
1.9038-1.9652	0.2353	176	0.2204	2494	X-RAY DIFFRACTION	100
1.9652-2.0355	0.2369	131	0.2085	2569	X-RAY DIFFRACTION	100
2.0355-2.117	0.2747	127	0.2004	2560	X-RAY DIFFRACTION	100
2.117-2.2133	0.2541	125	0.1944	2563	X-RAY DIFFRACTION	100
2.2133-2.33	0.2404	145	0.1928	2555	X-RAY DIFFRACTION	100
2.33-2.476	0.236	123	0.1978	2585	X-RAY DIFFRACTION	100
2.476-2.6671	0.2548	144	0.1976	2564	X-RAY DIFFRACTION	100
2.6671-2.9355	0.2404	155	0.213	2587	X-RAY DIFFRACTION	100
2.9355-3.3603	0.268	146	0.2084	2594	X-RAY DIFFRACTION	100
3.3603-4.2333	0.1951	152	0.1692	2623	X-RAY DIFFRACTION	100
4.2333-54.3358	0.1818	167	0.1694	2746	X-RAY DIFFRACTION	100

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	9.0477	2.8657	2.1508	8.395	2.9132	2.912	-0.0839	-0.1317	0.1411	-0.1763	0.123	-0.6779	-0.3787	0.0326	-0.0643	0.2846	-0.0077	-0.0148	0.2452	0.0492	0.2012	92.7121	10.6984	237.32
2	5.7393	-0.3939	-0.2252	5.073	-2.608	5.5533	-0.0756	0.4812	-0.1892	-0.2746	0.0869	0.2587	0.4792	-0.1453	-0.0674	0.1986	-0.0215	-0.0092	0.225	0.023	0.2286	85.8681	7.1787	236.7504
3	2.1743	-0.6802	-1.8026	5.9257	3.5728	4.2805	0.1806	0.2439	0.2507	0.0814	-0.1661	0.2454	-1.1447	-0.5018	0.0063	0.3536	0.0153	-0.0047	0.2403	0.036	0.314	84.375	18.3469	240.3859
4	2.6022	-3.6407	-0.6287	6.9905	3.6951	3.8311	-0.5581	-1.2363	1.1326	0.8015	0.8059	-0.5928	-0.9237	1.1289	-0.5309	0.752	-0.0042	-0.0992	0.5072	-0.0271	0.4129	92.5561	20.5375	251.7585
5	3.1475	-1.2013	-1.473	5.9035	-0.0257	0.7562	0.053	-0.9802	-1.5627	0.5989	-0.8111	-0.8721	0.4871	0.5166	0.4674	0.2814	0.0668	-0.0162	0.3405	0.1856	0.5511	102.1921	5.4638	242.2021
6	7.3585	1.8175	-0.9893	2.6563	-0.494	8.0116	0.0273	-0.3277	0.2739	0.364	-0.0995	0.1837	-0.42	0.1756	0.0566	0.2863	-0.0154	-0.0213	0.246	0.037	0.2946	95.0937	14.6646	238.0856
7	5.0735	-2.2121	-2.0969	1.0071	0.2919	3.9253	-0.0485	0.153	0.0972	0.6831	0.1939	-0.7208	-0.7145	0.4396	-0.1173	0.5761	-0.1019	-0.0844	0.2558	-0.0041	0.3055	88.8566	13.6916	265.1026
8	2.7033	-0.332	1.3213	2.3467	-1.4182	2.6901	-0.1048	-0.1933	0.2175	0.8293	0.1959	0.3116	-0.5202	-0.282	0.0547	0.5038	0.0493	0.066	0.2555	0.0313	0.2837	81.4968	14.0102	260.5558
9	6.065	-1.178	0.329	5.1805	-1.2102	4.4705	-0.1875	0.0966	0.3019	-0.2554	0.0457	-0.4722	-0.6772	0.4925	0.0548	0.3726	-0.1193	-0.0098	0.3153	-0.002	0.2924	92.0528	8.286	267.2563
10	3.7831	-3.1709	1.7356	3.2358	-1.5248	4.0541	-0.5635	-0.7754	-0.3931	0.9081	0.535	0.4832	0.4072	-0.3439	-0.0093	0.3922	-0.0048	0.072	0.3243	0.0144	0.3485	69.8834	-4.2882	241.614
11	2.1289	-0.5043	-1.7708	7.2372	-0.3634	8.4042	-0.6642	0.0222	0.2509	0.3693	0.2451	0.9222	-0.5332	-1.105	0.3675	0.2848	0.0384	0.0081	0.4246	-0.0037	0.4354	63.4259	4.3832	239.6353
12	6.563	0.1702	2.6782	2.0264	-0.3684	3.2314	-0.1746	-0.1139	-0.0073	0.3863	0.0366	-0.1065	0.1476	-0.0281	0.0969	0.3036	-0.0055	0.0223	0.218	0.0166	0.2488	77.9145	1.0889	240.8903
13	8.157	6.6226	1.3207	5.2298	1.0859	0.1464	0.3722	-1.1416	-1.2231	0.7987	-0.2435	-0.8293	0.2111	0.0954	-0.1673	0.7707	0.0834	-0.1036	0.6378	0.1397	0.6257	83.6093	-8.0677	249.5864
14	9.0862	-3.7399	-1.807	9.6091	-5.0442	9.5122	-0.1677	-0.4807	-0.2315	0.3803	0.4227	-0.3307	0.1008	-0.0184	-0.1495	0.4082	-0.0589	0.0208	0.398	0.0468	0.3393	64.9976	-10.2907	248.9768
15	1.1441	0.4656	0.541	6.0664	0.0349	6.7466	-0.0753	0.1466	0.0218	-0.0045	0.1689	-0.4596	0.1978	0.1542	-0.1395	0.3168	-0.0234	0.0125	0.239	0.0228	0.2479	74.9623	-7.4718	240.4192
16	2.7375	-0.6773	2.0354	6.1141	1.4463	7.7193	0.0112	-0.3808	0.6367	0.3587	0.0145	-0.5975	-0.0872	0.43	-0.01	0.2583	-0.0724	-0.0782	0.2107	0.0406	0.2946	71.6443	25.4877	237.1273
17	2.6172	0.5156	-0.9028	5.8338	-3.7655	3.2034	-0.0194	-0.05	0.0585	-0.0134	-0.2644	-0.1908	0.1608	0.4127	0.2701	0.1644	-0.0056	0.002	0.2584	0.0042	0.3043	71.671	16.8441	235.4215
18	3.2715	-4.3801	3.5333	7.3493	-7.623	8.3792	-0.1347	-0.3244	-0.4331	0.5194	0.5862	1.297	-0.0967	-0.6145	-0.3236	0.5331	0.0096	0.0952	0.4939	-0.0147	0.3491	62.7096	19.5378	247.5358
19	5.921	1.0417	1.2898	7.6581	1.185	7.0899	-0.0387	-0.4958	0.4429	0.6869	-0.262	-0.403	-0.858	0.0726	0.2942	0.3444	-0.0108	-0.0571	0.2583	0.0087	0.3188	67.7415	30.9175	237.2724

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'V' and (resid 1 through 10 )
2	X-RAY DIFFRACTION	2	chain 'V' and (resid 11 through 31 )
3	X-RAY DIFFRACTION	3	chain 'V' and (resid 32 through 52 )
4	X-RAY DIFFRACTION	4	chain 'V' and (resid 53 through 63 )
5	X-RAY DIFFRACTION	5	chain 'V' and (resid 64 through 73 )
6	X-RAY DIFFRACTION	6	chain 'V' and (resid 74 through 85 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1 through 25 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 26 through 63 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 64 through 85 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 10 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 11 through 18 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 19 through 53 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 54 through 63 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 64 through 73 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 74 through 86 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 25 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 26 through 52 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 53 through 63 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 64 through 85 )

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