PDB-8h5v: Crystal structure of the FleQ domain of Vibrio cholerae FlrA

ID or keywords:

Entry

Database: PDB / ID: 8h5v

Title

Crystal structure of the FleQ domain of Vibrio cholerae FlrA

Components

flagellar regulatory protein A

Keywords

TRANSCRIPTION / Sigma54 dependent transcription regulator

Function / homology

Function and homology information

sequence-specific DNA binding / regulation of DNA-templated transcription / ATP binding
Similarity search - Function

Biological species

Vibrio cholerae O395 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Dasgupta, J. / Chakraborty, S.

Funding support

India, 1items

Citation

Journal: Febs Lett. / Year: 2023
Title: The N-terminal FleQ domain of the Vibrio cholerae flagellar master regulator FlrA plays pivotal structural roles in stabilizing its active state.
Authors: Chakraborty, S. / Agarwal, S. / Bakshi, A. / Dey, S. / Biswas, M. / Ghosh, B. / Dasgupta, J.

History

Deposition	Oct 14, 2022	Deposition site: PDBJ / Processing site: PDBE
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8h5v.cif.gz	209.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8h5v.ent.gz	170.4 KB	Display	PDB format
PDBx/mmJSON format	8h5v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8h5v_validation.pdf.gz	466.4 KB	Display	wwPDB validaton report
Full document	8h5v_full_validation.pdf.gz	471.2 KB	Display
Data in XML	8h5v_validation.xml.gz	20.8 KB	Display
Data in CIF	8h5v_validation.cif.gz	29 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h5/8h5v ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h5v	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	#190 - Oct 2015 Two-component Systems similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: flagellar regulatory protein A

B: flagellar regulatory protein A

C: flagellar regulatory protein A

D: flagellar regulatory protein A

hetero molecules

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

1

A: flagellar regulatory protein A

hetero molecules

defined by author
Evidence: homology
14.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: flagellar regulatory protein A

hetero molecules

defined by author
14.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: flagellar regulatory protein A

defined by author
14.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: flagellar regulatory protein A

hetero molecules

defined by author
14.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.059, 66.471, 68.044
Angle α, β, γ (deg.)	90.00, 92.51, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-226- HOH

#1: Protein	flagellar regulatory protein A Mass: 14183.222 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: EYB64_02180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7Z8DVG5
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.93 Å³/Da / Density % sol: 36.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium sulfate 0.1M bis-Tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97893 Å / Relative weight: 1
Reflection	Resolution: 2→48.48 Å / Num. obs: 28994 / % possible obs: 98.9 % / Redundancy: 2.8 % / CC_1/2: 0.999 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2→2.05 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2154 / CC_1/2: 0.661

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: other

Resolution: 2→33.989 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 24.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.219	2003	6.91 %
R_work	0.1702	-	-
obs	0.1737	28982	98.69 %

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→33.989 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3829	0	25	152	4006

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3919
X-RAY DIFFRACTION	f_angle_d	1.203	5307
X-RAY DIFFRACTION	f_dihedral_angle_d	14.794	1443
X-RAY DIFFRACTION	f_chiral_restr	0.057	606
X-RAY DIFFRACTION	f_plane_restr	0.006	686

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 (%)
2.0001-2.0501	0.3249	140	0.259	1941	X-RAY DIFFRACTION	100
2.0501-2.1055	0.313	148	0.2396	1950	X-RAY DIFFRACTION	99
2.1055-2.1674	0.273	141	0.2188	1922	X-RAY DIFFRACTION	100
2.1674-2.2374	0.2851	145	0.215	1901	X-RAY DIFFRACTION	100
2.2374-2.3173	0.3018	146	0.2163	1928	X-RAY DIFFRACTION	99
2.3173-2.4101	0.2613	142	0.2022	1932	X-RAY DIFFRACTION	99
2.4101-2.5197	0.274	142	0.1969	1948	X-RAY DIFFRACTION	99
2.5197-2.6525	0.2488	143	0.1973	1907	X-RAY DIFFRACTION	99
2.6525-2.8187	0.2701	144	0.1965	1935	X-RAY DIFFRACTION	99
2.8187-3.0362	0.2438	145	0.189	1924	X-RAY DIFFRACTION	99
3.0362-3.3415	0.2183	132	0.1691	1927	X-RAY DIFFRACTION	98
3.3415-3.8244	0.2006	143	0.1519	1930	X-RAY DIFFRACTION	98
3.8244-4.8162	0.1742	148	0.136	1908	X-RAY DIFFRACTION	97
4.8162-33.9	0.1837	144	0.1506	1926	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	7.1609	-4.539	-5.0337	4.8478	5.0056	5.3043	-0.4911	-0.3552	-0.0755	0.3655	0.1162	0.3909	0.403	0.2616	0.6631	0.3641	0.0042	-0.0315	0.3647	0.0359	0.3693	3.6855	2.3968	14.1385
2	6.528	-3.4567	1.0475	3.4504	-0.1098	2.784	-0.0668	-0.229	0.3415	0.1511	0.0733	-0.2545	-0.1494	-0.0035	-0.0228	0.3407	-0.0191	-0.0032	0.2622	-0.0063	0.2832	-0.0022	6.7897	10.8869
3	8.3914	1.1113	0.9913	2.006	-0.3611	8.631	0.2978	-0.2528	0.0741	0.1572	-0.0735	-0.1596	-0.2618	0.2406	-0.1226	0.3297	0.0083	-0.0518	0.2339	-0.0199	0.3065	10.2955	0.1893	17.5857
4	8.198	0.0461	-1.2689	5.3363	0.3801	5.4016	0.1897	0.3819	-0.8313	-0.1023	-0.0552	-0.5004	0.4086	0.3044	-0.1459	0.3757	0.0376	-0.0844	0.3069	-0.0514	0.4591	8.4113	-8.8948	11.8569
5	6.9723	-6.0054	7.0411	5.1544	-6.1722	7.4306	0.2877	0.1683	0.0089	-0.2008	-0.3082	0.2248	0.4438	-0.3827	0.1344	0.3072	-0.0365	-0.055	0.4271	0.0235	0.5146	-5.1569	-5.8895	8.1469
6	5.9662	-5.5626	5.7814	5.0894	-5.367	5.6101	0.2084	-0.8491	-0.8702	0.3901	0.4092	0.4328	0.0857	-1.0457	-0.8398	0.4478	-0.095	0.0041	0.4246	0.0605	0.4615	-7.7071	-5.3228	18.7905
7	6.7342	6.2783	4.5539	7.1814	5.3448	3.9994	-0.3457	-0.9424	1.1164	0.0241	-1.7163	1.7413	-1.2135	-0.5479	1.8121	1.3462	0.2384	-0.0507	1.182	0.0433	0.8848	-2.9074	-4.9828	29.9992
8	6.4255	-0.0302	-1.9752	5.4768	1.0526	3.5272	-0.0674	-0.9228	0.2039	0.6892	0.2114	-0.2582	-0.1137	0.4107	-0.1787	0.4398	0.0358	-0.1181	0.5049	-0.0358	0.3041	21.3089	12.4606	34.8358
9	3.5799	0.5202	0.7073	4.4729	4.5415	6.0202	0.0516	-0.3918	0.1146	0.1351	-0.3619	0.8348	0.3351	-0.5318	0.2423	0.3602	-0.0277	-0.0469	0.4129	-0.0584	0.4058	9.0545	14.8282	31.2673
10	9.2167	-6.1253	-2.4532	8.3909	3.9321	3.3605	0.2459	0.2455	0.3331	-0.8659	-0.1818	-0.0996	-0.5499	0.0845	-0.2025	0.4477	-0.0548	-0.0587	0.345	0.016	0.287	19.0522	22.4676	23.5408
11	7.1174	2.5289	-1.8989	8.3615	4.1878	6.2781	0.6237	-0.5067	0.8372	0.911	-0.2261	-1.203	-0.0746	0.521	-0.2849	0.5447	-0.1827	-0.014	0.4329	0.0212	0.3359	16.8063	15.5115	2.3275
12	9.1632	-4.0808	-4.3503	5.4248	3.3901	4.0648	0.3197	-0.0009	0.1662	0.4219	-0.2631	0.0482	-0.2894	0.2067	-0.0171	0.3241	-0.0942	0.0476	0.3549	0.0124	0.2376	8.4107	12.0797	-2.5334
13	8.7962	-3.6194	-3.0513	4.4058	5.7546	8.0257	0.1115	-0.7813	0.1288	1.0307	0.0352	-0.1704	-0.2671	0.9407	-0.0756	0.5348	-0.1751	0.0605	0.4988	0.1095	0.3641	14.7576	12.2245	2.2246
14	6.99	-4.3919	-0.8601	4.0592	2.3866	4.2271	-0.0135	-1.6382	0.7323	1.3028	0.3186	-0.2171	-0.287	0.3943	-0.2186	0.8134	-0.24	0.0077	0.7032	-0.0174	0.4319	19.6582	20.1376	6.7502
15	3.25	0.5564	4.268	5.6416	4.9245	8.7623	0.7764	-1.4507	1.6859	1.1788	-0.0688	1.1112	-1.9352	0.6447	-0.6828	0.9524	-0.2737	0.2986	0.6021	-0.1323	0.7276	10.9431	30.2725	1.0687
16	4.7759	-3.9748	-0.7969	4.7191	2.3675	2.1863	0.1694	-1.114	0.8966	1.4683	0.0561	-1.0421	-0.394	0.2835	0.5518	1.1503	-0.4793	-0.1058	0.7376	0.0045	0.5965	23.0155	30.0799	6.0004
17	0.6791	-2.1053	0.8557	6.6167	-2.2076	4.6054	-0.6023	-0.0955	0.1946	0.7597	0.2372	-0.4007	-1.5493	0.643	0.2989	0.4848	-0.2085	-0.0746	0.4855	0.0497	0.3761	24.106	21.5557	-1.7868
18	5.3109	0.2919	3.2866	2.9175	-0.2301	2.0593	0.1692	0.3603	1.4709	0.03	-0.1336	0.2303	-0.5551	0.5253	0.0594	0.5865	-0.1989	0.1137	0.5457	0.0618	0.5883	18.8299	28.8454	-6.5929
19	8.0947	6.4828	1.753	5.3412	1.1019	0.7719	-0.1695	0.6644	0.593	-0.1799	0.1707	0.8468	0.0136	-0.0078	-0.149	0.3851	-0.0324	0.0207	0.4751	0.0765	0.4559	15.177	19.6408	-11.5271
20	5.2853	3.4632	6.8112	5.9221	3.9778	8.9942	0.2869	1.2316	0.4637	-0.4908	-0.1077	-0.8805	-0.2611	0.5753	-0.279	0.3823	0.0151	0.0717	0.5465	0.0826	0.3934	24.7015	13.3957	-10.0945
21	6.1739	1.4466	0.5069	3.9313	4.0351	4.3108	0.5883	0.2334	-0.1982	0.1033	1.0141	-2.9119	0.9494	0.1411	-1.3622	1.0421	-0.1358	-0.0163	1.1006	-0.2248	1.4926	34.1505	12.3125	-0.5044
22	7.0188	-4.9529	0.9564	3.7271	-0.0259	2.4781	0.0266	-0.1675	0.0936	-0.3022	0.0032	-0.2693	-0.287	-0.0579	-0.1206	0.3448	-0.0283	0.0036	0.2589	-0.0342	0.484	-12.1559	36.4997	21.2737
23	5.5434	-4.7715	-0.7235	4.077	0.6861	0.7957	0.3341	0.51	-0.1421	-0.0718	-0.4011	0.3323	-0.1418	0.2955	-0.0961	0.36	-0.0246	0.0271	0.4696	-0.0012	0.5529	-12.761	34.8683	17.0158
24	2.2942	0.1007	-0.3804	2.4225	0.5684	4.8021	0.0773	0.1123	-0.1505	-0.5734	0.1504	-0.7899	0.035	0.077	-0.1843	0.5088	0.0583	0.1239	0.3335	-0.0221	0.5947	-4.7947	29.5346	13.9465
25	7.2232	0.0816	-1.2825	5.6411	-1.7222	3.1441	0.0309	-0.6435	-0.2026	-0.3612	0.0014	-1.2575	-0.3068	0.7498	0.0802	0.429	-0.0297	0.1017	0.4197	-0.0057	0.7792	2.9608	33.4559	20.7047
26	7.4039	-1.3287	-0.2833	4.0236	1.9486	6.5875	-0.2525	-0.008	1.2427	-0.9308	-0.2845	-0.7501	-1.4226	0.2635	0.3003	0.7148	-0.0182	0.0543	0.3226	0.0254	0.9366	-3.1799	45.8807	17.0609

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 92 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 93 through 102 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 103 through 119 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 120 through 125 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 41 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 42 through 97 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 98 through 123 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 13 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 14 through 26 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 27 through 35 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 36 through 53 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 54 through 62 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 63 through 71 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 72 through 80 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 81 through 92 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 93 through 102 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 103 through 119 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 120 through 124 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3 through 26 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 27 through 35 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 36 through 53 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 54 through 89 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 90 through 120 )

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Yorodumi