PDB-8ih8: anti-sigmaF factor and Anti-sigmaF factor antagonist complex(usfx...

ID or keywords:

Entry

Database: PDB / ID: 8ih8

Title

anti-sigmaF factor and Anti-sigmaF factor antagonist complex(usfx-RsfB)

Components

Anti-sigma-F factor RsbW
Anti-sigma-F factor antagonist RsfB

Keywords

TRANSCRIPTION / tetramer / complex

Function / homology

Function and homology information

anti-sigma factor antagonist activity / sigma factor antagonist activity / hydrolase activity / negative regulation of DNA-templated transcription / nucleotide binding / regulation of DNA-templated transcription / ATP binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Chen, Y.J. / Su, D.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: High resolutions crystal structure of anti-sigmaF factor and Anti-sigmaF factor antagonist complex(usfx-RsfB)
Authors: Chen, Y.J. / Su, D.

History

Deposition	Feb 22, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ih8.cif.gz	204.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8ih8.ent.gz	164.8 KB	Display	PDB format
PDBx/mmJSON format	8ih8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ih8_validation.pdf.gz	470.3 KB	Display	wwPDB validaton report
Full document	8ih8_full_validation.pdf.gz	478 KB	Display
Data in XML	8ih8_validation.xml.gz	22.7 KB	Display
Data in CIF	8ih8_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/8ih8 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/8ih8	HTTPS FTP

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Related structure data

Similar structure data	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	#183 - Mar 2015 Phototropin similarity (4)

Deposited unit

A: Anti-sigma-F factor antagonist RsfB

C: Anti-sigma-F factor RsbW

B: Anti-sigma-F factor antagonist RsfB

D: Anti-sigma-F factor RsbW

hetero molecules

56.8 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

Unit cell

Length a, b, c (Å)	50.425, 77.928, 133.530
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Anti-sigma-F factor antagonist RsfB / Anti-anti-sigma F factor RsfB Mass: 12808.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: rsfB, Rv3687c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGE1
#2: Protein	Anti-sigma-F factor RsbW / Anti-sigma-F factor UsfX / Regulator of SigF / Sigma-F anti-sigma factor RsbW Mass: 15569.563 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: rsbW, usfX, Rv3287c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGX7
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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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: 46.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05M HEPES pH7.5 0.2M KCl 35.5% v/v pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 36351 / % possible obs: 99.3 % / Redundancy: 12.7 % / R_merge(I) obs: 0.057 / Net I/σ(I): 42.7
Reflection shell	Resolution: 2→2.06 Å / Num. unique obs: 21537 / CC_1/2: 0.15

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→33.65 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.215	2000	5.51 %
R_work	0.1804	-	-
obs	0.1824	36275	99.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→33.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3645	0	6	267	3918

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3733
X-RAY DIFFRACTION	f_angle_d	1.39	5088
X-RAY DIFFRACTION	f_dihedral_angle_d	14.454	534
X-RAY DIFFRACTION	f_chiral_restr	0.067	642
X-RAY DIFFRACTION	f_plane_restr	0.011	660

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 (%)
2-2.05	0.2723	136	0.1986	2325	X-RAY DIFFRACTION	97
2.05-2.1	0.2523	142	0.1969	2433	X-RAY DIFFRACTION	100
2.1-2.17	0.2273	140	0.1835	2404	X-RAY DIFFRACTION	100
2.17-2.24	0.2083	141	0.1743	2408	X-RAY DIFFRACTION	100
2.24-2.32	0.2003	141	0.179	2428	X-RAY DIFFRACTION	100
2.32-2.41	0.2583	142	0.1818	2430	X-RAY DIFFRACTION	100
2.41-2.52	0.238	143	0.192	2451	X-RAY DIFFRACTION	100
2.52-2.65	0.2783	142	0.1944	2430	X-RAY DIFFRACTION	100
2.65-2.82	0.2306	142	0.2027	2447	X-RAY DIFFRACTION	100
2.82-3.03	0.2612	143	0.2033	2442	X-RAY DIFFRACTION	100
3.03-3.34	0.2124	144	0.1885	2467	X-RAY DIFFRACTION	100
3.34-3.82	0.1905	144	0.1787	2474	X-RAY DIFFRACTION	100
3.82-4.81	0.1919	146	0.1526	2500	X-RAY DIFFRACTION	99
4.81-33.65	0.1828	154	0.1721	2636	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	3.5537	2.7263	-1.5533	6.5623	-2.4399	4.3159	0.0759	0.0874	0.3544	0.0005	0.2169	0.4931	-0.314	-0.2353	-0.3559	0.2178	-0.022	0.0231	0.3175	-0.0237	0.2488	-4.4075	-11.7376	-14.9598
2	2.2491	1.2324	-0.5724	4.3024	-1.1805	2.5943	-0.0757	0.1724	0.2091	-0.3813	0.2438	0.4847	0.0032	-0.2435	-0.1407	0.1932	0.0443	-0.0095	0.2383	-0.0115	0.2045	1.4573	-6.1436	-15.5395
3	9.2393	4.4943	-4.6442	4.5553	-4.7002	4.8185	0.2879	-0.3183	0.1976	0.3145	-0.2263	1.1116	-0.6719	-0.8978	-0.2026	0.384	0.0625	0.0192	0.3408	-0.0777	0.3227	-4.3728	-4.9754	-7.4482
4	6.4743	1.4767	-1.9135	6.2445	-2.1604	2.5836	0.0455	-0.3658	-0.1363	0.1797	0.1479	0.1254	-0.2844	-0.838	-0.1917	0.1957	-0.0064	-0.0389	0.2847	0.0326	0.279	0.4784	-14.6102	-7.335
5	5.1777	5.2799	-1.8206	5.5216	-2.5559	4.0809	-0.4319	0.5849	-0.0922	-0.1911	0.4984	-0.5463	0.0839	0.1114	-0.0043	0.272	0.0256	-0.0114	0.2008	-0.0006	0.2126	8.1443	-5.9917	-19.9438
6	6.0417	1.1333	-2.4468	5.4115	-2.1329	1.5484	0.5552	-1.1915	0.1382	1.0355	-0.5223	0.1114	-0.5694	0.324	-0.0894	0.3103	-0.0874	-0.0084	0.3298	-0.0657	0.2432	6.6999	-4.0736	-4.3659
7	2.8022	1.0226	-0.7095	4.2467	1.251	9.0255	0.4426	-0.5328	-0.1184	0.4318	-0.0334	-0.2945	-0.519	0.0649	-0.1563	0.242	-0.0577	-0.0232	0.3268	0.0203	0.2513	4.5328	-14.1867	-1.325
8	3.6226	-0.4066	-1.1823	3.2186	0.1569	5.2009	-0.1007	-0.3258	0.0777	0.2824	-0.1144	-0.0937	-0.029	0.3948	0.135	0.2031	0.0002	0.004	0.2128	0.024	0.2441	16.2716	-10.2076	-12.7624
9	4.4364	3.1629	3.7553	4.2321	6.0613	8.9968	-0.0563	-0.7347	-0.4773	0.2387	-0.1598	-0.2337	0.3749	0.2336	-0.0031	0.2113	-0.0379	-0.0095	0.4486	0.0358	0.4202	10.8635	-16.2178	-7.6934
10	7.2414	-6.4293	-2.6148	7.6914	4.4138	3.1939	-0.9329	-1.3165	-1.4939	1.093	0.4049	-0.4132	1.0014	0.5765	0.244	0.3544	0.0051	0.0578	0.3462	0.1542	0.5917	4.8265	-23.8089	-7.5046
11	3.1931	-0.8587	-1.0898	3.8444	0.0233	4.538	-0.1274	-0.1384	0.0023	-0.0186	0.1105	-0.1267	0.0654	0.2113	-0.0232	0.1385	-0.0069	-0.0343	0.2087	-0.0007	0.1711	16.3461	5.1853	-30.2017
12	2.028	-1.6236	-0.1923	2.7568	1.6044	3.0667	0.0734	-0.1111	0.0736	0.2948	-0.0778	-0.2452	0.1069	-0.0489	0.0247	0.1952	-0.0284	0.0033	0.222	0.021	0.1936	15.3408	3.482	-20.058
13	7.319	-3.3538	-4.0027	3.569	3.3663	8.3006	0.2324	0.241	0.1754	-0.229	-0.0198	-0.3352	-0.1642	0.4583	-0.1836	0.2443	-0.0196	-0.0234	0.2038	0.0184	0.2011	20.5265	11.4582	-25.994
14	2.1985	-0.7206	0.4627	5.1243	-0.2426	2.2308	0.1912	-0.1592	-0.0229	-0.1105	-0.1438	-0.2802	-0.0464	0.1581	-0.0952	0.245	-0.0323	-0.0122	0.2656	0.0185	0.1877	21.6524	9.6	-12.5189
15	7.3355	-0.9375	-1.2836	2.4007	2.7268	6.2973	-0.206	-0.3618	0.7069	0.5526	0.2983	-0.6207	-0.0731	-0.0218	-0.1347	0.1993	-0.0559	-0.0348	0.2734	0.0052	0.2045	21.4888	17.2193	-18.6751
16	4.5899	1.7552	2.6202	6.6301	5.117	4.319	0.1124	-0.0061	-0.5162	0.212	0.538	-1.1987	-0.5864	0.5006	-0.8986	0.5013	0.041	0.0338	0.5545	-0.0463	0.5355	26.2767	-6.6001	-42.4169
17	4.1318	-0.2474	-0.1516	1.8849	-0.9967	3.2918	0.1797	-0.1522	-0.5551	0.2897	-0.1088	-0.2249	0.5603	-0.1204	-0.0694	0.2958	0.031	-0.0062	0.2207	-0.0144	0.2313	18.5156	-16.9088	-54.6354
18	3.5137	0.1662	-0.8677	9.8721	1.9768	1.9888	0.174	0.4984	-0.3503	-0.3734	-0.036	-0.6335	0.2654	0.5875	-0.1494	0.3307	0.1196	-0.0027	0.3396	-0.0062	0.3038	23.7166	-13.7026	-61.56
19	3.301	-1.381	-0.3318	5.9112	1.8291	3.6803	-0.0478	0.0552	-0.4084	0.2293	0.0665	-0.1237	0.4844	-0.007	-0.1067	0.2168	-0.0068	-0.0167	0.1726	0.014	0.239	14.1149	-15.2628	-56.7248
20	6.4535	1.4594	2.056	7.3662	4.4217	2.9476	0.1096	0.7826	-0.1099	-1.0369	0.0011	-0.0253	-0.3065	0.4739	-0.0452	0.339	0.0099	-0.034	0.2464	0.0382	0.2096	14.5054	-7.0624	-64.0564
21	1.7422	-0.7364	0.0465	2.5921	0.6547	2.8452	-0.0656	0.3596	-0.201	-0.0897	-0.2129	0.2714	0.297	-0.169	0.2116	0.2435	-0.0548	-0.0394	0.211	-0.0157	0.2056	9.1289	-14.9651	-60.7832
22	7.0945	-2.535	0.4833	8.0481	4.4922	3.181	-0.1961	-0.0871	-0.2114	-0.3356	-0.0347	0.5432	-0.1519	-0.8713	0.0491	0.2337	-0.0221	-0.0131	0.2763	-0.0235	0.273	2.6905	-6.1209	-58.3155
23	5.691	-0.1951	0.0851	2.3244	-3.354	9.0997	0.0628	0.6146	-0.9338	0.0238	0.0325	0.869	0.8364	-0.8371	-0.0847	0.3946	-0.1161	-0.0172	0.3405	-0.0823	0.4624	5.7733	-20.9866	-60.8275
24	3.342	-3.2355	-1.6823	3.6111	0.8224	9.325	0.2602	0.572	1.531	-0.344	-0.0317	1.0313	-0.5629	-1.0249	0.0961	0.4344	0.1866	-0.0495	0.4739	-0.0214	0.6085	3.6414	15.9687	-33.4173
25	7.5433	-2.7343	-3.9703	6.9081	2.438	2.3583	-0.1753	-0.1189	0.3958	0.1705	0.4048	-0.6429	0.1063	0.5117	-0.2889	0.1635	-0.0166	-0.0587	0.2621	-0.0207	0.2049	18.9214	10.9999	-39.3427
26	3.0449	1.1372	0.7658	3.7396	0.0869	3.6743	0.0319	0.0207	-0.1846	0.0385	-0.0667	0.109	0.3641	-0.3128	0.054	0.2043	-0.0009	-0.0216	0.1795	-0.0223	0.1583	11.3564	1.5502	-39.9415
27	9.3619	7.7802	-1.6094	7.7503	-1.6324	1.9273	-0.2165	0.1949	0.0781	-0.3314	0.1748	0.0014	0.1591	0.067	0.0325	0.1721	0.0358	-0.0032	0.1716	-0.0292	0.1937	14.1536	5.5188	-48.6283
28	3.1824	2.7151	-2.8413	3.8543	-1.207	3.8872	0.328	-0.3583	0.6832	0.3912	0.0256	0.3668	-0.1341	-0.4393	-0.3355	0.2578	-0.0082	-0.0108	0.4036	0.0127	0.2526	6.5015	12.6077	-39.4511
29	2.884	4.0782	-4.0505	7.3833	-4.1139	7.0769	0.2258	-0.0625	0.7314	0.2445	0.1943	0.4913	-0.0596	-0.1699	-0.3525	0.1607	0.0128	-0.0154	0.2025	-0.0243	0.1717	9.6687	13.7424	-44.9
30	4.0211	4.9147	2.5188	6.7612	3.4115	1.9683	-0.2464	0.448	0.1945	-0.5136	0.2187	0.309	-0.0988	0.2521	-0.0255	0.2954	0.0296	0.0033	0.3593	0.0209	0.2059	16.1451	15.203	-59.1336
31	2.2592	0.0966	1.0584	3.528	1.5949	4.0671	0.2587	0.1681	0.014	-0.3933	-0.2613	0.3872	0.2675	-0.5853	0.0345	0.2911	0.0254	-0.0536	0.3025	0.0141	0.243	6.5442	10.276	-55.1995
32	2.6565	-0.7907	-2.5645	5.2092	2.6389	3.1744	0.3218	0.7072	1.1749	-0.4471	-0.0322	0.1512	-0.705	0.3464	-0.2298	0.3441	0.0283	0.0025	0.309	0.0236	0.4313	22.6743	25.6039	-53.228
33	8.1556	4.7273	-2.9366	7.2499	-2.8523	5.0384	0.2991	-0.3794	0.3194	0.1604	-0.2006	0.6029	0.3472	-0.1932	-0.0583	0.1986	-0.0306	0.0042	0.2737	-0.0171	0.1918	5.5624	12.3323	-47.3327

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 44 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 45 through 54 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 55 through 60 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 61 through 74 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 75 through 83 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 84 through 100 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 101 through 107 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 108 through 117 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 12 through 46 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 47 through 67 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 68 through 93 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 94 through 120 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 121 through 140 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid -1 through 7 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 8 through 30 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 31 through 44 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 45 through 60 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 61 through 74 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 75 through 89 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 90 through 100 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 101 through 116 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 12 through 17 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 18 through 25 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 26 through 46 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 47 through 72 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 73 through 83 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 84 through 93 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 94 through 103 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 104 through 120 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 121 through 129 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 130 through 141 )

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