PDB-26jl: Crystal structure of the AAA+ domain of Vibrio cholerae FlrA

ID or keywords:

Entry

Database: PDB / ID: 26jl

Title

Crystal structure of the AAA+ domain of Vibrio cholerae FlrA

Components

Flagellar regulatory protein A

Keywords

TRANSCRIPTION / Flagellar Synthesis / bacterial enhancer binding protein / AAA+ domain

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: 3.2 Å

Authors

Dasgupta, J. / Sen, U. / Das, R.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Insights into the open spiral hexameric structure of the AAA+ domain of FlrA, the Master regulator of flagellar synthesis in Vibrio cholerae
Authors: Das, R. / Pal, A. / Chakraborty, S. / Sen, U. / Dasgupta, J.

History

Deposition	May 1, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 3, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	26jl.cif.gz	630.3 KB	Display	PDBx/mmCIF format
PDB format	pdb26jl.ent.gz	527.5 KB	Display	PDB format
PDBx/mmJSON format	26jl.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/6j/26jl ftp://data.pdbj.org/pub/pdb/validation_reports/6j/26jl	HTTPS FTP

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Related structure data

Related structure data	8h5v
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

E: Flagellar regulatory protein A

F: Flagellar regulatory protein A

hetero molecules

191 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking, Dynamic Light Scattering experiments proved hexamer

Unit cell

Length a, b, c (Å)	101.165, 101.165, 49.909
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	1
Space group name H-M	P1

#1: Protein	Flagellar regulatory protein A Mass: 29092.422 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: flrA, VC0395_A1721 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AM86
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 260 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.53 Å³/Da / Density % sol: 51.46 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Potassium Formate, 20% (w/v) PEG 3350, 5% MPD

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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: 0.98 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 25, 2025
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 3.2→49 Å / Num. obs: 27109 / % possible obs: 99.1 % / Redundancy: 2 % / CC_1/2: 0.996 / Net I/σ(I): 8.5
Reflection shell	Resolution: 3.2→3.42 Å / Num. unique obs: 4750 / CC_1/2: 0.468

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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: ALPHAFOLD

Resolution: 3.2→9.98 Å / SU ML: 0.47 / Cross valid method: NONE / σ(F): 0.44 / Phase error: 28.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.295	3624	6.69 %
R_work	0.22	-	-
obs	0.225	27109	99.1 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→9.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12210	0	1040	583	13833

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	13227
X-RAY DIFFRACTION	f_angle_d	2.374	17318
X-RAY DIFFRACTION	f_dihedral_angle_d	25.346	5023
X-RAY DIFFRACTION	f_chiral_restr	0.089	1860
X-RAY DIFFRACTION	f_plane_restr	0.014	2226

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 (%)
3.201-3.3293	0.2552	120	0.2261	1922	X-RAY DIFFRACTION	100
3.3293-3.3771	0.3342	156	0.2272	1956	X-RAY DIFFRACTION	100
3.3771-3.4278	0.3653	144	0.2103	1920	X-RAY DIFFRACTION	100
3.4278-3.4817	0.339	168	0.2308	1932	X-RAY DIFFRACTION	100
3.4817-3.5391	0.3375	132	0.2548	2118	X-RAY DIFFRACTION	100
3.5391-3.6005	0.5019	132	0.2549	1778	X-RAY DIFFRACTION	100
3.6005-3.6664	0.2343	132	0.1318	2028	X-RAY DIFFRACTION	100
3.6664-3.7373	0.1675	156	0.1437	2052	X-RAY DIFFRACTION	100
3.7373-3.8142	0.4725	144	0.3089	1902	X-RAY DIFFRACTION	100
3.8142-3.8977	0.4041	144	0.2567	2000	X-RAY DIFFRACTION	100
3.8977-3.9891	0	132	0	1638	X-RAY DIFFRACTION	91
3.9891-4.0898	0.3119	132	0.3041	1860	X-RAY DIFFRACTION	93
4.0898-4.2014	0.5015	144	0.21	2072	X-RAY DIFFRACTION	98
4.2014-4.3263	0.3573	144	0.231	1866	X-RAY DIFFRACTION	100
4.3263-4.4675	0.3687	144	0.2039	1902	X-RAY DIFFRACTION	100
4.4675-4.6292	0.3479	108	0.2065	2030	X-RAY DIFFRACTION	100
4.6292-4.8171	0.2294	156	0.1867	1860	X-RAY DIFFRACTION	100
4.8171-5.0398	0.2452	132	0.2316	2054	X-RAY DIFFRACTION	100
5.0398-5.3104	0.2248	144	0.2101	1968	X-RAY DIFFRACTION	100
5.3104-5.6504	0.5265	144	0.2128	1946	X-RAY DIFFRACTION	99
5.6504-6.0986	0.3046	120	0.2515	1902	X-RAY DIFFRACTION	100
6.0986-6.7343	0.4854	168	0.2378	2006	X-RAY DIFFRACTION	100
6.7343-7.7601	0.234	114	0.2243	1914	X-RAY DIFFRACTION	98
7.7601-9.98	0	138	0	1954	X-RAY DIFFRACTION	98

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	-0.0309	-0.0019	0.0007	-0.0187	-0.021	-0.0081	-0.0469	-0.1503	0.0444	0.1344	0.025	0.001	0.1379	0.0407	0	-0.2536	-0.5781	0.176	-0.6358	0.2365	-0.0257	-16.411	-39.853	-1.033
2	0.0016	0.0031	0	-0.0011	0.0018	0.0024	-0.0093	-0.0033	0.0036	0.0127	0.012	-0.0055	0.0205	-0.0734	0	0.2238	-0.1026	0.2992	0.1715	-0.0001	0.1296	-12.667	-19.681	11.164
3	0.0303	0.0281	-0.0639	0.03	-0.0305	0.0307	0.1203	-0.0507	0.0824	0.1017	0.3199	0.3007	0.0772	-0.4247	0	-0.0253	-0.1905	-0.142	-0.4269	-0.4221	-0.1691	-17.33	-26.986	-1.425
4	-0.0201	0.0079	0.0086	-0.0091	-0.0021	-0.0003	-0.0502	-0.0359	-0.0264	0.1349	0.0377	-0.039	-0.0039	0.0202	-0	0.1604	0.2965	-0.1213	-0.6145	0.3408	-0.1431	25.885	-33.793	4.342
5	-0.0061	-0.0114	-0.002	0.0065	-0.0367	0.0167	0.01	-0.0444	0.002	0.001	0.035	-0.0242	0.1455	0.0801	0	0.2481	0.1673	0.0735	0.3025	0.019	0.0672	15.895	-25.249	23.425
6	-0.0111	0.0267	-0.0173	-0.0201	-0.0133	0.0067	-0.0385	0.1341	0.0109	0.2354	-0.1534	-0.0676	0.1504	0.1532	-0	-0.0154	-0.123	0.1503	-0.1469	0.0348	-0.064	20.721	-17.611	18.109
7	0.0117	-0.0023	-0.0044	0.0005	-0.0056	0.0102	0.0757	0.0361	0.1034	0.0328	0.0701	-0.0129	-0.098	-0.0798	-0	0.1276	0.0456	0.0421	0.0251	-0.1325	-0.0254	20.973	-25.889	1.599
8	0.0228	-0.0153	-0.0028	0.0037	0.0181	-0	-0.0858	-0.1084	0.0153	-0.0516	0.0501	0.0111	0.2844	0.0236	0	0.1189	0.0056	0.033	0.0669	0.0485	0.1378	5.948	-42.477	-7.409
9	-0.0115	0.009	0.002	-0.0262	-0.0094	-0.0026	0.0802	-0.1065	-0.0565	0.079	0.0472	-0.0105	-0.138	0.0856	-0	-0.611	0.2045	-0.1485	0.0528	0.0631	0.0178	41.496	5.109	16.136
10	0.003	0.0043	0.0006	-0.0021	-0.0028	0.0048	0.1039	-0.0797	0.0021	0.0328	0.1525	-0.0339	-0.0007	0.0591	0	0.172	-0.3121	0.2968	0.2769	0.0425	-0.0456	26.039	0.561	34.319
11	-0.0223	-0.0109	-0.001	0.0077	-0.0238	0.0116	-0.1538	-0.0976	0.0807	0.0201	0.2152	-0.0589	0.0083	0.1393	-0	-0.0687	0.2649	-0.1617	-0.1412	0.3	-0.2687	23.984	9.931	26.188
12	0.0339	0.0108	0.0173	-0.0155	0.0184	0.0226	0.3387	-0.1426	-0.1514	-0.0945	0.0249	-0.0209	0.3192	0.1421	-0	-0.2655	-0.0824	0.0843	0.0388	0.0624	-0.017	37.001	-7.575	4.541
13	-0.0327	-0.0063	-0.0087	-0.0125	-0.0012	-0.0028	-0.017	-0.1506	-0.0567	0.1741	0.0006	0.0279	-0.1065	-0.0858	0	-0.0395	-0.3551	-0.1131	-0.4407	-0.1867	-0.024	16.403	39.844	23.902
14	0.0037	0.0066	0.0098	-0.001	-0.0052	0.0013	0.0561	-0.0347	-0.017	0.0716	0.0999	0.0217	-0.0291	0.0613	-0	0.3597	0.0029	-0.0717	0.1819	0.0693	0.1085	12.762	20.302	42.713
15	-0.0024	-0.0107	0.0181	-0.0154	-0.0065	0.0044	0.0939	-0.2402	0.1023	-0.0932	-0.2014	0.0009	-0.1708	0.0442	0	-0.1204	-0.206	0.2555	-0.1571	0.3894	-0.3793	4.853	26.758	34.755
16	-0.0173	0.0125	-0.0309	0.0495	0.0188	-0.0111	0.1299	0.2088	-0.0733	0.1791	0.2433	-0.1304	0.008	0.3359	0	-0.0095	-0.1562	0.022	-0.3606	0.1256	0.0064	25.051	28.251	12.866
17	-0.0202	-0.0012	-0.0017	-0.0195	0.0045	-0.0001	-0.014	-0.1341	-0.0062	0.0913	-0.0674	-0.0898	0.0268	-0.099	0	0.0665	0.3385	0.0372	-0.6629	-0.1031	0.0322	-26.339	34.118	-17.687
18	-0.0054	0.0006	0.0074	0.0096	0.0033	0.0031	0.0999	-0.0708	-0.0149	0.0332	0.1012	-0.0085	-0.0867	-0.0172	-0	0.3107	0.083	-0.0253	0.2438	0.0038	0.0685	-11.206	21.211	1.112
19	-0.0151	0.0294	0.0207	-0.0146	0.0166	0.0059	0.1143	0.1533	0.0533	0.1791	-0.1717	0.0052	-0.0821	-0.1453	0	-0.0234	0.1302	-0.2353	-0.2357	0.3015	-0.2455	-20.73	17.582	-6.85
20	0.0023	-0.0213	-0.0567	-0.0136	-0.0231	-0.0041	0.1995	-0.0869	0.2062	-0.1502	0.317	-0.2122	-0.3243	0.1193	-0	-0.1673	0.1468	-0.2005	-0.0668	0.0822	-0.1284	-11.949	35.832	-28.767
21	-0.0173	0.0174	-0.0004	-0.0085	-0.0099	0.0105	0.0345	-0.0913	-0.008	0.1155	0.001	-0.0809	0.0589	-0.0797	0	-0.2852	-0.0231	0.0417	0.1941	-0.0016	0.0322	-42.74	-5.694	-9.361
22	0.0026	-0.0119	-0.0001	-0.0005	0.0113	0.0015	0.1092	-0.1171	-0.0209	0.0481	0.057	-0.0294	-0.0068	-0.0385	0	0.2264	-0.0963	0.03	0.3017	-0.0518	0.1617	-23.971	0.916	9.439
23	-0.0271	0	0.026	-0.0065	0.0153	0.012	-0.1425	-0.0558	-0.0458	0.027	0.2328	-0.0348	0.0399	-0.1358	-0	-0.4944	0.0891	-0.388	-0.0464	-0.0124	-0.2151	-24.562	-10.477	-0.53
24	0.0192	0.0212	0.0071	0.0073	-0.023	-0.02	0.3424	-0.0464	0.1086	-0.0494	0.0111	-0.017	-0.2519	-0.1187	0	-0.0376	-0.0079	-0.0425	0.0969	-0.0311	0.017	-40.117	11.92	-22.912

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 140:199 )	A	140 - 199
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 200:215 )	A	200 - 215
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 216:385 )	A	216 - 385
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 140:186 )	B	140 - 186
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 187:235 )	B	187 - 235
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 236:294 )	B	236 - 294
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 295:333 )	B	295 - 333
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 334:385 )	B	334 - 385
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 140:205 )	C	140 - 205
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 206:245 )	C	206 - 245
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 246:294 )	C	246 - 294
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 295:385 )	C	295 - 385
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 140:199 )	D	140 - 199
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 200:235 )	D	200 - 235
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 236:294 )	D	236 - 294
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 295:385 )	D	295 - 385
17	X-RAY DIFFRACTION	17	( CHAIN E AND RESID 140:199 )	E	140 - 199
18	X-RAY DIFFRACTION	18	( CHAIN E AND RESID 200:235 )	E	200 - 235
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 236:294 )	E	236 - 294
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 295:385 )	E	295 - 385
21	X-RAY DIFFRACTION	21	( CHAIN F AND RESID 140:199 )	F	140 - 199
22	X-RAY DIFFRACTION	22	( CHAIN F AND RESID 200:235 )	F	200 - 235
23	X-RAY DIFFRACTION	23	( CHAIN F AND RESID 236:309 )	F	236 - 309
24	X-RAY DIFFRACTION	24	( CHAIN F AND RESID 310:385 )	F	310 - 385

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