PDB-6ghb: Crystal structure of Spx in complex with YjbH (oxidized)

ID or keywords:

Entry

Database: PDB / ID: 6ghb

Title

Crystal structure of Spx in complex with YjbH (oxidized)

Components

Regulatory protein Spx
UPF0413 protein GK0824

Keywords

PROTEIN BINDING / Regulatory protein spx Adaptor protein YjbH

Function / homology

Function and homology information

negative regulation of DNA-templated transcription / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.104 Å

Authors

Awad, W. / Logan, D.T. / von Wachenfeldt, C.

Citation

Journal: Structure / Year: 2019
Title: Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx.
Authors: Awad, W. / Al-Eryani, Y. / Ekstrom, S. / Logan, D.T. / von Wachenfeldt, C.

History

Deposition	May 6, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2019	Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ghb.cif.gz	324.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6ghb.ent.gz	266.2 KB	Display	PDB format
PDBx/mmJSON format	6ghb.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/gh/6ghb ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6ghb	HTTPS FTP

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Related structure data

Related structure data	6ghoC C: citing same article (ref.)
Similar structure data	6bzn-2 6bzi-1 4d7a-1 4rdi-1 6yjo-d 3enl-d 6gja-d 6gho-d 6eo5-2 3lyk-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Regulatory protein Spx

B: UPF0413 protein GK0824

C: Regulatory protein Spx

D: UPF0413 protein GK0824

hetero molecules

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

1

A: Regulatory protein Spx

B: UPF0413 protein GK0824

hetero molecules

defined by author&software
Evidence: gel filtration
49.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Regulatory protein Spx

D: UPF0413 protein GK0824

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.596, 88.704, 117.467
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Regulatory protein Spx Mass: 15638.970 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: spxA, yjbD, BSU11500 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O31602
#2: Protein	UPF0413 protein GK0824 Mass: 33716.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria) Strain: HTA426 / Gene: GK0824 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q5L1S1
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Na-HEPES pH 7.5, MgCl2 and PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→48.429 Å / Num. obs: 16640 / % possible obs: 99.17 % / Redundancy: 4.1 % / CC_1/2: 0.994 / Net I/σ(I): 10.97
Reflection shell	Resolution: 3.1→3.2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1613 / CC_1/2: 0.609 / % possible all: 98.59

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: 000)	refinement
Coot		model building
XDS		data scaling
PHENIX		phasing
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 3.104→48.429 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 28.24

	R_factor	Num. reflection	% reflection
R_free	0.2659	3056	9.89 %
R_work	0.2216	-	-
obs	0.226	16640	99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.104→48.429 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6140	0	2	13	6155

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6286
X-RAY DIFFRACTION	f_angle_d	1.107	8522
X-RAY DIFFRACTION	f_dihedral_angle_d	21.257	3836
X-RAY DIFFRACTION	f_chiral_restr	0.055	949
X-RAY DIFFRACTION	f_plane_restr	0.006	1091

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 (%)
3.1043-3.1528	0.3818	128	0.3484	1254	X-RAY DIFFRACTION	96
3.1528-3.2045	0.3419	132	0.3525	1264	X-RAY DIFFRACTION	100
3.2045-3.2597	0.3657	131	0.3186	1267	X-RAY DIFFRACTION	99
3.2597-3.319	0.3396	145	0.3262	1278	X-RAY DIFFRACTION	100
3.319-3.3828	0.3576	148	0.2994	1262	X-RAY DIFFRACTION	100
3.3828-3.4518	0.2906	133	0.2777	1290	X-RAY DIFFRACTION	100
3.4518-3.5269	0.3419	155	0.2786	1278	X-RAY DIFFRACTION	100
3.5269-3.6089	0.3533	121	0.2546	1251	X-RAY DIFFRACTION	100
3.6089-3.6991	0.2864	151	0.2409	1317	X-RAY DIFFRACTION	100
3.6991-3.7991	0.2841	132	0.2271	1244	X-RAY DIFFRACTION	100
3.7991-3.9108	0.2803	141	0.2251	1272	X-RAY DIFFRACTION	99
3.9108-4.037	0.3127	139	0.2128	1280	X-RAY DIFFRACTION	100
4.037-4.1812	0.2483	136	0.2079	1264	X-RAY DIFFRACTION	99
4.1812-4.3485	0.2588	148	0.2025	1257	X-RAY DIFFRACTION	99
4.3485-4.5463	0.2161	126	0.1859	1276	X-RAY DIFFRACTION	99
4.5463-4.7858	0.216	153	0.1662	1258	X-RAY DIFFRACTION	99
4.7858-5.0853	0.1994	123	0.1732	1272	X-RAY DIFFRACTION	99
5.0853-5.4775	0.2396	145	0.1997	1278	X-RAY DIFFRACTION	99
5.4775-6.0278	0.2801	139	0.1977	1246	X-RAY DIFFRACTION	99
6.0278-6.8979	0.2418	138	0.2166	1271	X-RAY DIFFRACTION	99
6.8979-8.6824	0.231	133	0.1875	1270	X-RAY DIFFRACTION	99
8.6824-48.4348	0.2062	159	0.1834	1197	X-RAY DIFFRACTION	96

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	4.4037	-1.6499	-2.7489	4.8951	0.7539	8.9561	0.0068	-1.1057	0.2277	1.1807	-0.1966	-0.3555	0.2612	1.0236	0.0102	0.7515	-0.1238	-0.1047	1.0782	0.1686	0.3306	108.6843	3.9709	-57.0972
2	3.6408	-2.4171	-2.793	4.1881	1.6816	7.8071	-0.2412	-0.7171	-0.1145	0.2212	-0.0086	-0.2166	-0.5749	0.9887	0.2605	0.68	-0.0088	-0.1676	0.684	0.1351	0.5027	107.0989	2.8447	-54.0225
3	8.2304	0.7287	-3.554	4.0437	0.5417	7.9579	0.0068	1.3314	-0.1786	0.0243	0.0917	-0.53	0.1014	0.9624	0.002	0.7586	-0.0378	0.0732	0.7942	-0.0462	0.3427	111.0411	4.6612	-70.6742
4	1.8811	0.4848	0.2299	3.2422	-1.5544	0.8509	-0.502	-0.1493	0.2702	0.0648	0.3908	0.444	-0.7481	-0.2615	0.053	1.4035	0.038	-0.2764	0.7374	0.1418	0.7629	107.2944	17.0802	-67.3269
5	4.2895	-1.1929	-5.0866	3.4101	2.0936	6.1576	0.6084	0.0223	0.8308	0.4081	1.4586	-0.9164	-0.0378	1.1334	-2.0232	0.8064	-0.1991	0.0131	0.8197	-0.1589	0.8512	116.5721	21.0993	-68.6698
6	5.2303	2.2288	-6.6344	7.1328	-4.0133	8.6148	0.0748	0.0421	-0.9215	0.7065	-0.868	-0.8691	-1.0167	1.362	0.4229	0.7155	-0.3529	-0.0779	0.6775	-0.0556	0.6595	120.0404	11.9659	-71.0518
7	6.5113	5.5946	-7.0453	9.6838	-4.5352	8.1757	1.1759	-0.7908	-0.2258	0.724	0.3732	0.2268	-2.2231	0.6925	-1.1247	1.246	-0.3755	-0.1837	0.8995	0.1418	0.5162	113.313	14.3954	-60.5852
8	2.0566	3.0032	-2.9527	3.1215	-1.5398	8.6557	0.3592	1.6364	-1.2336	0.5111	0.1967	-0.2964	-0.5213	-0.0019	-0.1198	0.5403	-0.1167	0.0568	0.6511	0.1077	0.3926	100.9087	5.6681	-62.1996
9	8.8802	2.3324	-4.1172	6.3899	2.118	9.6007	0.6559	1.3401	1.3898	1.1115	0.2452	0.6724	-1.4928	-1.4759	-0.6763	0.7757	-0.0784	0.1895	0.5216	0.3617	0.4795	93.5952	6.5779	-57.9283
10	8.0384	0.8801	8.2051	5.4711	0.7209	8.7548	0.15	-1.3259	-1.2347	-0.145	0.2048	0.3601	-0.1618	-0.33	-0.0575	0.5689	-0.0649	0.1943	0.7623	0.0653	0.4406	82.6646	-4.4792	-68.1617
11	6.695	-3.4844	-2.1257	7.8796	2.0766	4.5049	-0.1364	-0.2946	0.0594	0.0748	-0.0248	0.1899	-0.0913	-0.1023	0.0168	0.2188	-0.0918	0.0452	0.4482	-0.016	0.2518	90.5853	6.6869	-79.3974
12	1.8388	-1.8169	-0.6932	6.5804	2.507	7.916	-0.1909	0.9787	-1.2238	-0.3049	0.346	0.0714	0.7847	0.2406	-0.1764	0.5301	-0.1179	0.076	0.816	-0.2962	0.7215	94.3516	-6.2276	-96.1901
13	5.3567	0.8759	0.7546	5.5872	-0.2491	5.5516	-0.4171	0.2584	-0.2821	-0.4339	0.7658	-0.4524	0.0899	1.0276	-0.3213	0.4114	-0.0293	0.0488	0.7632	-0.1217	0.2942	106.2705	2.1127	-85.2723
14	4.699	1.1489	-1.9403	4.3791	-0.7305	5.0419	-0.0922	0.6302	0.417	-0.3787	0.1841	0.5139	-0.3977	-0.5478	0.0118	0.2885	-0.0366	-0.0985	0.3822	-0.0656	0.3113	86.7208	11.9501	-86.5342
15	7.9929	-2.1608	-2.5767	3.8385	-0.5699	6.5111	0.1776	-1.0176	-0.3536	0.9997	-0.8378	-1.0206	-0.3802	0.8644	-0.2018	0.6462	-0.2107	-0.1749	1.1256	0.2332	0.486	109.0514	46.7847	-5.5265
16	5.4681	-1.5985	-1.4971	3.8165	-0.0489	5.7858	0.2832	-1.7969	-0.1254	0.9197	-0.3095	-0.2707	-0.3428	1.1256	-0.0658	0.7601	-0.1865	-0.0782	1.1307	0.1396	0.4282	107.2994	45.9915	-2.3735
17	5.6778	-0.5207	1.4545	6.4599	1.3171	2.5072	0.4653	-0.2305	-1.694	1.5012	-0.0002	0.4293	0.8609	0.4387	-0.2301	0.7706	0.0786	-0.0744	0.3083	-0.0847	0.4527	112.2038	46.7662	-19.0056
18	5.3485	2.2354	2.386	4.6455	-0.4535	4.1043	0.5065	1.3881	1.1891	0.7916	0.4264	1.6512	-1.7349	-0.2386	-0.9451	0.8603	0.1545	0.161	1.3407	0.2768	0.4743	106.1821	56.3838	-18.9108
19	6.2384	5.4391	-1.7102	2.0003	-4.1134	1.9915	0.7932	-1.2179	1.1784	2.5389	-0.0969	0.1094	-2.8017	-0.3492	-0.8048	1.3066	-0.1305	0.1179	0.7115	-0.0371	0.6162	117.5687	65.7845	-11.7257
20	3.9924	4.5677	-1.5106	9.7253	-4.3782	8.7636	0.3176	-0.2392	0.7626	0.7114	0.2824	-0.4559	-0.7711	-0.2323	-0.6455	0.3684	-0.0377	0.0425	0.7126	-0.1065	0.5132	117.6242	57.5677	-17.4988
21	6.1025	2.87	4.1983	5.5708	1.1384	2.994	0.2476	0.6044	-0.1221	-0.194	0.0108	0.0536	-0.4387	-0.2906	-0.2585	0.6001	-0.0695	0.1353	0.9515	-0.0201	0.338	94.107	46.4519	-11.4115
22	5.3645	-2.7742	-2.605	5.2632	-0.7845	7.4167	-0.3308	0.4369	-0.1171	0.2765	-0.0591	0.185	-0.5352	0.6359	0.2775	0.3446	-0.1057	0.0021	0.6264	0.0207	0.3256	90.7656	49.8661	-27.5199
23	3.9803	0.6682	-1.7136	0.7802	-2.0824	7.5532	-1.167	1.153	-1.5471	-0.0438	-1.2068	-0.0417	1.7541	-0.0391	1.062	0.6614	-0.1517	-0.1821	1.5619	-0.5433	0.4795	94.6325	34.6741	-44.4862
24	6.0147	1.3515	-1.053	3.7731	0.5216	5.2318	-0.124	0.4515	-0.5929	-0.0832	0.1304	-0.0808	-0.1012	0.0986	-0.0231	0.3503	0	-0.0464	0.5005	-0.0287	0.2843	100.6248	43.4628	-30.2956
25	4.8107	0.3431	-1.1426	4.8419	1.4233	3.8394	-0.0874	1.2016	0.7318	-0.8863	-0.1626	0.3655	-0.9217	-0.5015	0.2371	0.5184	0.0748	-0.1428	0.9918	0.0631	0.5161	87.5829	58.5478	-40.3887

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 10 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 48 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 60 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 75 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 76 through 85 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 86 through 93 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 94 through 106 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 107 through 113 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 114 through 124 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 23 through 63 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 64 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 187 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 188 through 293 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 0 through 10 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 11 through 38 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 39 through 47 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 48 through 57 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 58 through 67 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 68 through 93 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 94 through 122 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 21 through 63 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 64 through 108 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 109 through 215 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 216 through 292 )

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