PDB-6g1n: Crystal structure of the Burkholderia Pseudomallei antitoxin HicB

ID or keywords:

Entry

Database: PDB / ID: 6g1n

Title

Crystal structure of the Burkholderia Pseudomallei antitoxin HicB

Components

antitoxin HicB

Keywords

ANTITOXIN / 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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 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 / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6g1n.cif.gz	235.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6g1n.ent.gz	193 KB	Display	PDB format
PDBx/mmJSON format	6g1n.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/g1/6g1n ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1n	HTTPS FTP

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Related structure data

Related structure data	SASDD45C SASDD55C 6g1cSC 6g26C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1880 6ijh-d 6f2u-d 4llj-d 4yqh-d 5xc1-d 2oup-d 4lm1-d 4qdm-d 5uwf-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDD45associated SAS data, The SAXS data of the antitoxin HicB

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: antitoxin HicB

B: antitoxin HicB

C: antitoxin HicB

D: antitoxin HicB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Analytical SEC showed a tetrameric association, native gel electrophoresis, Native mass spectrometry showed the presence of a tetramer in the gas phase, SAXS, SAXS showed ...Evidence: gel filtration, Analytical SEC showed a tetrameric association, native gel electrophoresis, Native mass spectrometry showed the presence of a tetramer in the gas phase, SAXS, SAXS showed the formation of a tetramer

Unit cell

Length a, b, c (Å)	62.580, 62.580, 173.490
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	antitoxin HicB Mass: 15762.726 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSS0391 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63NA5
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.67 Å³/Da / Density % sol: 53.6 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1 M NaOAc, 0.02M CaCl2.dH20 15% MPD

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.85→42.472 Å / Num. obs: 56223 / % possible obs: 99 % / Redundancy: 4.7 % / B_iso Wilson estimate: 57.88 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.05854 / R_rim(I) all: 0.066 / Net I/σ(I): 9.84
Reflection shell	Resolution: 1.85→1.917 Å / Redundancy: 4.7 % / R_merge(I) obs: 3.521 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5547 / CC_1/2: 0.129 / R_rim(I) all: 3.962 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
xia2		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6G1C

6g1c

Resolution: 1.85→42.472 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2414	2712	4.86 %
R_work	0.203	-	-
obs	0.2049	55828	98.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→42.472 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4120	0	22	187	4329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4466
X-RAY DIFFRACTION	f_angle_d	0.867	6121
X-RAY DIFFRACTION	f_dihedral_angle_d	19.264	2737
X-RAY DIFFRACTION	f_chiral_restr	0.058	701
X-RAY DIFFRACTION	f_plane_restr	0.006	802

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 (%)
1.8504-1.8841	0.4657	110	0.459	2513	X-RAY DIFFRACTION	88
1.8841-1.9203	0.4257	132	0.4257	2756	X-RAY DIFFRACTION	97
1.9203-1.9595	0.4293	136	0.3622	2806	X-RAY DIFFRACTION	99
1.9595-2.0021	0.38	140	0.3306	2800	X-RAY DIFFRACTION	99
2.0021-2.0487	0.3727	143	0.3	2804	X-RAY DIFFRACTION	99
2.0487-2.0999	0.3086	140	0.2747	2811	X-RAY DIFFRACTION	99
2.0999-2.1567	0.281	168	0.2577	2807	X-RAY DIFFRACTION	99
2.1567-2.2202	0.2928	155	0.2434	2758	X-RAY DIFFRACTION	99
2.2202-2.2918	0.2581	136	0.2317	2814	X-RAY DIFFRACTION	100
2.2918-2.3737	0.2896	176	0.2267	2807	X-RAY DIFFRACTION	100
2.3737-2.4688	0.2732	155	0.2242	2791	X-RAY DIFFRACTION	99
2.4688-2.5811	0.2582	139	0.2119	2833	X-RAY DIFFRACTION	100
2.5811-2.7172	0.301	152	0.2091	2842	X-RAY DIFFRACTION	100
2.7172-2.8874	0.2607	127	0.2279	2803	X-RAY DIFFRACTION	99
2.8874-3.1102	0.2598	148	0.2187	2840	X-RAY DIFFRACTION	100
3.1102-3.4231	0.2374	137	0.2135	2834	X-RAY DIFFRACTION	100
3.4231-3.9182	0.25	152	0.1864	2810	X-RAY DIFFRACTION	100
3.9182-4.9353	0.1665	122	0.1626	2852	X-RAY DIFFRACTION	99
4.9353-42.4833	0.2051	144	0.1754	2835	X-RAY DIFFRACTION	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	3.3311	0.3565	1.7465	3.9855	1.2822	7.9784	0.2482	-0.0405	0.1381	-0.0665	-0.1591	0.0937	-0.2498	-0.8528	-0.1232	0.3537	-0.0382	0.0444	0.4537	-0.0048	0.3966	54.7484	64.8159	19.8738
2	2.212	0.874	4.2063	3.3506	3.5006	8.4203	0.0745	-0.0805	-0.1207	0.3281	-0.0437	0.0303	0.6578	-0.1277	-0.0068	0.4833	-0.0953	0.0285	0.4817	0.019	0.4351	57.7624	55.1605	20.1482
3	5.2029	-4.0268	-0.9314	4.56	1.6108	4.1421	-0.4722	-0.7015	0.4227	0.2477	0.5125	-0.0964	-0.0224	0.0005	-0.0972	0.3784	0.0812	-0.0152	0.4297	-0.016	0.4295	80.7929	53.3168	11.8152
4	2.8349	0.157	-1.3682	3.3482	-2.5296	7.9333	-0.1623	-0.046	-0.0733	-0.0492	0.1976	-0.0715	0.8182	0.076	-0.075	0.4137	-0.045	0.0084	0.3331	-0.0423	0.3915	96.1308	23.4738	-20.0923
5	2.7934	0.8096	-2.6298	1.7825	-3.9135	7.9614	-0.0493	0.2832	-0.0495	-0.2737	0.127	0.2027	0.3572	-0.8947	-0.038	0.4543	-0.1254	-0.0103	0.4515	-0.024	0.4817	86.3793	26.2478	-20.4701
6	4.817	-4.1353	-1.8947	5.5211	-0.2082	5.0256	0.5148	0.378	0.0878	-0.8037	-0.5074	-0.3123	0.1095	0.1444	-0.0222	0.4548	0.0629	0.0026	0.4062	-0.0073	0.4337	84.1934	49.0722	-12.2958
7	8.945	0.1038	-2.0121	9.1172	-1.1256	8.5939	0.33	0.4241	-0.427	-0.0054	-0.0849	1.3085	0.8629	-1.0883	-0.151	0.4234	-0.0725	-0.0923	0.4261	-0.0717	0.3686	54.3347	55.3912	1.2076
8	4.2474	1.8633	-4.0487	3.9762	-2.6487	4.0117	-0.3486	-0.3468	-0.7531	-0.3468	-0.1985	-0.3303	1.0793	0.6101	0.4416	0.5477	0.0154	-0.0264	0.3712	-0.0127	0.4991	62.9846	54.3638	0.0911
9	6.2628	0.9956	-5.6009	0.1023	-0.7084	5.13	0.4033	0.1705	1.4436	0.3647	0.3821	0.2115	-0.5826	-0.8668	-0.5763	0.5579	0.1232	0.0751	0.5564	0.0283	0.6074	60.5681	69.656	-5.5943
10	2.1596	-1.996	-2.4952	2.7187	0.1412	7.1045	0.2408	-0.0484	-0.0811	-0.0655	-0.1828	-0.0558	-0.5226	-0.4067	-0.1628	0.3836	0.067	-0.1292	0.3736	-0.0815	0.3749	58.5105	63.4054	0.9699
11	6.6428	0.3296	1.16	3.4802	0.2918	4.2632	0.7195	1.762	-0.1037	-2.4161	-1.0214	0.181	0.1235	-0.248	0.2834	0.9196	0.4118	-0.0017	0.7569	0.0009	0.5108	82.5086	52.3002	-21.1107
12	7.1518	0.1213	0.8036	8.2671	1.307	7.9733	-0.1189	0.2593	-0.8423	0.2575	0.3342	0.647	0.8796	-1.0377	-0.1306	0.3949	-0.0748	0.081	0.373	0.0748	0.3527	86.6526	23.0474	-1.4848
13	3.0526	2.5681	2.6521	4.5795	5.521	8.8183	-0.0269	-0.3648	-0.0602	-0.111	-0.1812	0.2739	-0.3186	-0.9372	0.1178	0.325	0.0321	0.0101	0.3912	0.058	0.4245	88.2337	32.3294	1.6195
14	3.9137	-3.579	0.2302	4.1982	0.7896	8.1556	-0.046	-0.7135	-0.2178	0.5658	0.4157	-0.354	1.6528	0.3287	-0.261	0.7792	0.105	0.0447	0.5338	0.0581	0.5349	95.9218	17.8681	-1.4647
15	9.3535	5.7364	2.1995	6.1162	3.4468	8.5501	-0.0893	0.4918	0.5923	-0.2433	0.163	0.5596	-0.5015	0.9512	-0.1013	0.4843	-0.0153	0.0496	0.404	0.0749	0.4728	95.9787	31.7137	-4.2012
16	4.7333	-4.8833	-2.419	5.2934	3.094	3.523	-0.2746	-0.5239	1.6706	-0.0005	0.5442	-1.2069	-0.485	0.1001	-0.4856	0.5608	0.0447	-0.0308	0.4011	-0.0927	0.7827	91.6314	52.6873	11.5835
17	3.7086	-0.7701	0.0871	4.6851	-0.4095	2.1348	-0.8495	-2.4737	-0.5429	1.9524	0.7994	0.2621	0.7687	0.2164	0.0059	0.9697	0.4799	0.0745	1.1619	0.0076	0.5565	82.3511	49.6526	22.7137

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 88 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 89 through 131 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 53 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 54 through 88 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 89 through 132 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 26 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 27 through 53 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 54 through 65 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 66 through 94 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 95 through 133 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 26 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 27 through 58 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 59 through 77 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 78 through 88 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 89 through 101 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 102 through 133 )

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