PDB-6luf: Trans-acting mutant Y290A of the central AAA+ domain of the flage...

ID or keywords:

Entry

Database: PDB / ID: 6luf

Title

Trans-acting mutant Y290A of the central AAA+ domain of the flagellar regulatory protein FlrC

Components

Flagellar regulatory protein C

Keywords

TRANSCRIPTION / Vibrio cholerae / Flagellar Synthesis / Mutation

Function / homology

Function and homology information

phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.45 Å

Authors

Dasgupta, J. / Chakraborty, S.

Citation

Journal: To Be Published
Title: Oligomerization of flagellar regulatory protein FlrC is essential for cis-mediated ATP binding while c-di-GMP prefers its monomeric state
Authors: Dasgupta, J. / Chakraborty, S.

History

Deposition	Jan 27, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6luf.cif.gz	679 KB	Display	PDBx/mmCIF format
PDB format	pdb6luf.ent.gz	565.8 KB	Display	PDB format
PDBx/mmJSON format	6luf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6luf_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6luf_full_validation.pdf.gz	2.3 MB	Display
Data in XML	6luf_validation.xml.gz	60.7 KB	Display
Data in CIF	6luf_validation.cif.gz	78.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lu/6luf ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6luf	HTTPS FTP

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Related structure data

Related structure data	6luaC 4qhsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7jwd-d 7jz5-d 6bti-d 5exs-d 6jdl-d 5o2k-4 7jvy-d 6j7e-d 5ajk-3 4fna-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

6luaC

4qhsS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Flagellar regulatory protein C

B: Flagellar regulatory protein C

C: Flagellar regulatory protein C

D: Flagellar regulatory protein C

E: Flagellar regulatory protein C

F: Flagellar regulatory protein C

G: Flagellar regulatory protein C

hetero molecules

214 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Flagellar regulatory protein C

hetero molecules

defined by author&software
Evidence: gel filtration
30.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Flagellar regulatory protein C

hetero molecules

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

3

C: Flagellar regulatory protein C

hetero molecules

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

4

D: Flagellar regulatory protein C

hetero molecules

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

5

E: Flagellar regulatory protein C

hetero molecules

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

6

F: Flagellar regulatory protein C

hetero molecules

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

7

G: Flagellar regulatory protein C

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.927, 154.127, 194.063
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Flagellar regulatory protein C Mass: 30102.564 Da / Num. of mol.: 7 / Mutation: Y390A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria) Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: flrC, VC0395_A1719 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3AHP1
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interest	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: 3.15 Å³/Da / Density % sol: 60.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% (w/v) PEG6000

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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: 0.979 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.45→48.01 Å / Num. obs: 32784 / % possible obs: 100 % / Redundancy: 7.2 % / CC_1/2: 0.99 / Net I/σ(I): 9.9
Reflection shell	Resolution: 3.45→3.64 Å / Num. unique obs: 4707 / CC_1/2: 0.811

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Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4QHS

4qhs

Resolution: 3.45→46.277 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.97

	R_factor	Num. reflection	% reflection
R_free	0.2341	1633	5 %
R_work	0.1877	-	-
obs	0.1901	32686	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.45→46.277 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13416	0	189	0	13605

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13861
X-RAY DIFFRACTION	f_angle_d	0.918	18796
X-RAY DIFFRACTION	f_dihedral_angle_d	15.622	5292
X-RAY DIFFRACTION	f_chiral_restr	0.036	2146
X-RAY DIFFRACTION	f_plane_restr	0.004	2415

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 (%)
3.4501-3.5516	0.3729	113	0.2894	2570	X-RAY DIFFRACTION	100
3.5516-3.6662	0.3045	158	0.2527	2536	X-RAY DIFFRACTION	100
3.6662-3.7972	0.3007	134	0.2256	2533	X-RAY DIFFRACTION	100
3.7972-3.9491	0.2494	134	0.2122	2568	X-RAY DIFFRACTION	100
3.9491-4.1288	0.2406	119	0.1974	2570	X-RAY DIFFRACTION	100
4.1288-4.3463	0.2125	135	0.19	2562	X-RAY DIFFRACTION	100
4.3463-4.6184	0.2084	126	0.1602	2566	X-RAY DIFFRACTION	100
4.6184-4.9746	0.2331	139	0.163	2603	X-RAY DIFFRACTION	100
4.9746-5.4745	0.2287	134	0.1749	2578	X-RAY DIFFRACTION	100
5.4745-6.265	0.2271	148	0.1856	2608	X-RAY DIFFRACTION	100
6.265-7.8868	0.1976	133	0.1702	2639	X-RAY DIFFRACTION	100
7.8868-46.277	0.1875	160	0.1454	2720	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	5.2819	1.3226	2.197	2.8435	-0.3973	4.7361	-0.4938	1.1173	-0.5748	-0.2009	0.4306	-0.0637	-0.055	0.5137	0.0503	0.45	-0.0135	0.0253	0.4562	-0.0576	0.3833	16.2392	61.664	-42.4437
2	3.7324	0.1845	-0.8025	2.5257	-1.5318	4.1143	0.0316	-0.1355	-0.1771	0.2341	-0.1675	-0.0665	0.1049	0.2052	0.1481	0.2828	-0.0088	0.0082	0.3036	0.0048	0.3462	27.1427	58.6058	-25.2628
3	1.3102	0.608	-0.2027	3.2682	0.2011	0.0507	0.1528	0.2883	0.1768	-0.1324	-0.174	0.0815	-0.0437	0.019	-0.0212	0.5858	-0.0129	-0.0722	0.4453	0.0646	0.399	10.5854	48.2877	-49.8213
4	6.0753	-1.389	1.0014	9.0563	4.5145	7.9945	0.0675	0.4132	-0.3148	0.1843	0.1825	0.4267	0.0429	0.4629	0.0098	0.5011	-0.056	-0.0216	0.3709	-0.0026	0.3756	10.7595	37.0594	-50.9913
5	3.8167	2.2422	-0.4328	1.7582	0.5062	2.2924	0.1121	0.0196	-0.3541	-0.0423	0.0283	0.0118	-0.1594	0.085	-0.0379	0.4993	0.054	-0.0998	0.4526	0.0154	0.4385	18.487	20.179	-45.1432
6	4.9241	-1.9107	-0.7113	2.3299	1.8758	4.8966	0.0857	-0.257	0.2096	0.0473	-0.026	-0.1638	0.3053	0.3453	-0.0259	0.3409	0.0439	-0.0101	0.3105	-0.018	0.3809	31.0137	30.948	-28.7932
7	0.9423	-0.3927	1.2922	2.2011	0.6064	2.0921	-0.1587	-0.0487	0.1902	0.3159	0.0508	0.3163	0.2841	-0.0672	0.0869	0.3803	0.0108	-0.0351	0.3931	0.0214	0.2893	15.4558	30.2536	-35.6653
8	5.1157	-1.9375	1.5615	4.4986	-1.5657	3.8951	0.0849	0.2059	-0.2283	-0.4034	0.1865	-0.0148	0.1477	-0.0256	-0.2629	0.3949	-0.0591	0.0543	0.3229	-0.0887	0.3959	11.1748	-0.5417	-34.698
9	6.5375	3.216	-1.5882	3.0352	-1.4819	0.6818	-0.1956	-0.6014	-0.8671	0.3628	-0.2901	-0.7689	-0.0718	0.3571	0.4972	0.788	-0.1435	0.0197	0.481	0.0388	0.453	16.1205	-7.8847	-13.2798
10	3.6596	-0.527	1.3224	3.9591	1.2266	1.9701	-0.0904	-0.0817	0.0466	-0.0381	-0.0094	-0.1166	-0.2351	-0.0391	0.0995	0.3274	0.0001	0.024	0.3538	0.0149	0.308	27.12	9.3731	-13.9604
11	1.0889	0.269	-0.5368	-0.0077	-0.3294	3.404	0.2028	0.1611	-0.2834	0.1375	-0.0334	-0.1637	0.1874	0.0593	-0.1905	0.6319	-0.0093	0.0227	0.3911	-0.0582	0.4361	10.6645	-11.6612	1.7853
12	9.7906	2.2505	2.2311	9.397	1.2436	6.3089	0.3435	-0.3218	-0.44	0.5945	-0.4918	-0.1975	0.5018	-0.5418	0.2037	0.5282	0.046	-0.0053	0.3461	0.0155	0.2889	10.6876	-12.2949	14.6732
13	4.5509	1.0482	-1.2065	1.5403	-1.2751	1.1044	-0.2106	-0.8486	0.1066	-0.0361	-0.0257	-0.0924	-0.0407	0.2874	0.244	0.5554	-0.025	-0.0208	0.441	-0.0386	0.4217	18.521	-1.6236	27.7505
14	4.5117	0.0766	1.8262	5.089	-2.1806	1.7251	-0.172	0.0667	0.417	0.0496	0.0028	-0.1722	-0.1167	0.3494	0.2169	0.3548	-0.0539	-0.0224	0.4928	-0.0404	0.3335	29.9958	10.805	14.1506
15	0.3504	0.7353	-0.7939	1.1954	-1.8411	3.1625	0.1212	0.0567	-0.2398	0.2348	-0.0047	0.2317	-0.4352	-0.2916	-0.0023	0.436	-0.0635	-0.0436	0.4518	-0.0696	0.4593	11.6145	5.9647	15.8065
16	4.379	1.3955	1.5085	3.7568	-0.0193	3.7766	0.0072	0.0252	-0.0932	0.3762	-0.1403	0.0393	0.2148	0.1122	0.1316	0.4285	0.0308	0.056	0.3647	0.0812	0.3071	11.2002	13.4176	45.7386
17	8.0847	-5.4233	-3.4913	3.7093	2.6305	6.2338	0.3527	-0.1846	0.3848	-0.1007	0.1922	-0.2476	-0.2225	0.1552	-0.6806	0.3306	0.0091	0.0233	0.404	-0.0168	0.3723	12.0432	36.1493	52.8058
18	2.2144	1.1566	-0.229	1.8013	-0.1985	4.2783	-0.02	0.0238	0.0403	-0.0197	0.0124	-0.0064	-0.0905	0.0223	0.0622	0.2869	0.0067	-0.0276	0.272	-0.003	0.3591	25.7744	32.1982	33.6208
19	1.4728	0.2776	-0.2404	5.235	1.6952	0.9218	0.1503	-0.2022	0.1411	0.2332	0.1245	0.1854	0.0548	0.1234	-0.2575	0.3626	0.012	0.0128	0.3242	-0.0277	0.2581	10.8457	55.1225	47.5992
20	4.5984	-1.3103	0.5461	1.9525	0.5049	0.5714	-0.1581	0.2568	0.7806	-0.0988	0.1403	-0.2332	-0.3151	0.0296	-0.0234	0.5751	0.0184	0.0845	0.5045	0.0271	0.4484	18.3423	74.5864	32.92
21	2.2417	-0.7473	-0.4341	2.9569	1.6934	2.7608	0.1	0.0637	-0.1604	-0.2095	0.0195	-0.2061	-0.1378	0.0696	-0.1336	0.3097	-0.0222	-0.0109	0.3275	0.0774	0.3585	24.8902	59.3583	24.9959
22	4.2837	0.9823	-3.2478	4.6349	-0.9695	6.8634	0.3971	-0.178	0.1323	0.3738	-0.0171	-0.4217	-0.881	0.106	-0.5097	0.5705	0.0743	-0.0547	0.3726	-0.0339	0.4267	11.0478	89.2178	14.4762
23	4.7794	0.0943	0.7426	2.4235	-0.2892	2.923	-0.0823	0.7323	0.4207	0.2685	-0.1801	-0.2326	0.0995	-0.0153	0.2228	0.5181	0.1247	0.0108	0.5185	0.0458	0.4499	16.4625	86.3996	-7.9085
24	3.9383	-0.7505	-0.8898	3.9168	-0.6688	0.8107	0.0363	0.1988	-0.1524	-0.1846	-0.1924	-0.3602	0.1209	0.1195	0.1865	0.3523	-0.0089	0.0437	0.5442	-0.0393	0.3452	31.0203	70.7339	-4.7376
25	6.9782	-0.5584	-4.3406	3.5633	1.3458	3.1224	0.0086	-1.1002	0.304	0.1047	-0.0211	-0.479	0.4408	0.5238	-0.2506	0.5095	0.1047	-0.0943	0.492	0.0834	0.3387	30.9136	69.0684	7.0616
26	0.9911	-0.9693	-1.0098	3.0877	-0.5056	1.3988	-0.1242	-0.1298	-0.1797	-0.089	0.0222	0.237	-0.0333	-0.3431	0.1431	0.3463	0.0544	0.0503	0.4626	0.0056	0.3013	15.5363	75.3178	-0.0732
27	3.7872	0.1337	-2.3908	2.8545	-0.0588	6.1078	0.2474	-0.3427	-0.2261	0.3737	-0.2923	-0.0815	-0.6853	-0.1184	0.0609	0.4482	-0.0094	-0.0509	0.3555	0.0914	0.3396	12.0717	81.7744	-28.5179
28	8.7369	-2.9401	-1.1745	2.1535	-0.6079	6.8307	-0.5842	0.4795	-0.2882	-0.8761	-0.2404	0.0766	-0.1147	-0.7878	0.3532	0.4731	-0.0491	0.0042	0.566	0.055	0.3205	8.8811	79.0686	-37.2593

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 130 through 174 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 175 through 292 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 293 through 346 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 347 through 376 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 130 through 182 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 183 through 259 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 260 through 305 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 306 through 376 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 131 through 174 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 175 through 292 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 293 through 350 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 351 through 376 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 131 through 182 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 183 through 274 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 275 through 305 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 306 through 376 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 131 through 149 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 150 through 292 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 293 through 376 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 131 through 182 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 183 through 305 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 306 through 376 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 131 through 174 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 175 through 236 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 237 through 259 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 260 through 305 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 306 through 361 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 362 through 376 )

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi