PDB-5x0o: Regulatory domain of AphB treated with Cumene hydroperoxide from ...

ID or keywords:

Entry

Database: PDB / ID: 5x0o

Title

Regulatory domain of AphB treated with Cumene hydroperoxide from Vibrio vulnificus

Components

LysR family transcriptional regulator

Keywords

TRANSCRIPTION / AphB / LysR-type / transcriptional regulator / tcpPH activation

Function / homology

Function and homology information

sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.402 Å

Authors

Song, S. / Park, N. / Ha, N.-C.

Citation

Journal: Mol. Cells / Year: 2017
Title: Crystal Structure of the Regulatory Domain of AphB from Vibrio vulnificus, a Virulence Gene Regulator
Authors: Park, N. / Song, S. / Choi, G. / Jang, K.K. / Jo, I. / Choi, S.H. / Ha, N.-C.

History

Deposition	Jan 22, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 10, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 24, 2017	Group: Database references
Revision 1.2	Nov 22, 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	5x0o.cif.gz	469.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5x0o.ent.gz	389.7 KB	Display	PDB format
PDBx/mmJSON format	5x0o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5x0o_validation.pdf.gz	459.3 KB	Display	wwPDB validaton report
Full document	5x0o_full_validation.pdf.gz	466.9 KB	Display
Data in XML	5x0o_validation.xml.gz	39 KB	Display
Data in CIF	5x0o_validation.cif.gz	52.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/5x0o ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x0o	HTTPS FTP

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Related structure data

Related structure data	5fhkSC 5x0nC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5fhk-1 5x0n-2 5x0n-3 6mlu-d 5x0n-1 6n9n-1 3gl1-1 2pju-1 3fzh-1 6rwz-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) 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

5fhkSC

5x0nC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LysR family transcriptional regulator

B: LysR family transcriptional regulator

C: LysR family transcriptional regulator

D: LysR family transcriptional regulator

E: LysR family transcriptional regulator

F: LysR family transcriptional regulator

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

1

A: LysR family transcriptional regulator

B: LysR family transcriptional regulator

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

2

C: LysR family transcriptional regulator

F: LysR family transcriptional regulator

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

3

D: LysR family transcriptional regulator

E: LysR family transcriptional regulator

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

Unit cell

Length a, b, c (Å)	124.844, 189.418, 57.424
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	LysR family transcriptional regulator Mass: 23402.980 Da / Num. of mol.: 6 / Fragment: UNP residues 88-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: JS86_04620 / Plasmid: pPROEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A087IWB4

#1: Protein

LysR family transcriptional regulator

Mass: 23402.980 Da / Num. of mol.: 6 / Fragment: UNP residues 88-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio vulnificus (bacteria) / Gene: JS86_04620 / Plasmid: pPROEX-HTa / Production host:

Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A087IWB4

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.78 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES (pH 7.5), 15% PEG 8000, 10% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 51444 / % possible obs: 99.7 % / Redundancy: 8.8 % / R_merge(I) obs: 0.122 / Net I/av σ(I): 13.44 / Net I/σ(I): 13.44
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 5.7 % / R_merge(I) obs: 0.433 / Mean I/σ(I) obs: 2.95 / Num. unique all: 2629 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
DENZO		data reduction
HKL-2000		data scaling
HKL-2000		data processing
Coot		model building
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FHK

5fhk

Resolution: 2.402→45.696 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 25.29

	R_factor	Num. reflection	% reflection
R_free	0.2562	2487	4.83 %
R_work	0.2086	-	-
obs	0.211	51444	95.1 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.402→45.696 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9374	0	0	0	9374

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9600
X-RAY DIFFRACTION	f_angle_d	0.556	13036
X-RAY DIFFRACTION	f_dihedral_angle_d	5.629	6219
X-RAY DIFFRACTION	f_chiral_restr	0.044	1471
X-RAY DIFFRACTION	f_plane_restr	0.004	1663

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 (%)
2.4019-2.4481	0.327	71	0.2784	1825	X-RAY DIFFRACTION	65
2.4481-2.498	0.3476	115	0.276	2222	X-RAY DIFFRACTION	78
2.498-2.5524	0.3383	125	0.2784	2379	X-RAY DIFFRACTION	86
2.5524-2.6117	0.2976	112	0.2846	2657	X-RAY DIFFRACTION	92
2.6117-2.677	0.3634	133	0.2805	2643	X-RAY DIFFRACTION	96
2.677-2.7494	0.323	155	0.2755	2795	X-RAY DIFFRACTION	98
2.7494-2.8303	0.3273	158	0.2622	2759	X-RAY DIFFRACTION	99
2.8303-2.9216	0.2968	134	0.2453	2846	X-RAY DIFFRACTION	99
2.9216-3.026	0.3078	139	0.2475	2830	X-RAY DIFFRACTION	99
3.026-3.1472	0.2609	138	0.2383	2803	X-RAY DIFFRACTION	100
3.1472-3.2904	0.277	144	0.2238	2841	X-RAY DIFFRACTION	100
3.2904-3.4638	0.2663	151	0.2162	2855	X-RAY DIFFRACTION	100
3.4638-3.6807	0.2585	144	0.1937	2845	X-RAY DIFFRACTION	100
3.6807-3.9648	0.2417	132	0.1827	2881	X-RAY DIFFRACTION	100
3.9648-4.3635	0.2144	168	0.1631	2868	X-RAY DIFFRACTION	100
4.3635-4.9942	0.1793	151	0.145	2894	X-RAY DIFFRACTION	100
4.9942-6.2895	0.2118	162	0.1805	2934	X-RAY DIFFRACTION	100
6.2895-45.704	0.2243	155	0.1783	3080	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	3.9568	-2.0738	2.5125	6.7657	-4.4492	6.2669	-0.032	-0.2552	0.0788	0.4359	-0.319	-0.471	0.0973	0.2081	0.2698	0.252	0.0064	0.0715	0.209	-0.0043	0.2397	1.4049	59.1137	-7.34
2	0.5466	0.4711	-0.4999	2.3778	0.157	1.9671	0.0036	-0.27	0.2499	-0.0452	-0.1919	-0.3916	-0.2544	0.229	0.0875	0.2022	0.0304	-0.0471	0.2445	0.0586	0.303	-1.6828	62.5729	-9.937
3	0.9256	-0.7622	0.6246	1.9837	-1.3294	1.025	0.0614	-0.1079	0.1647	0.0948	-0.0639	-0.0799	-0.0175	0.032	0.094	0.221	0.0101	0.0255	0.2644	-0.0033	0.3367	5.1812	58.7231	3.5668
4	1.8733	0.4938	-0.103	2.3858	0.8224	2.62	0.0948	-0.4774	-0.0861	-0.0185	-0.0019	-0.2332	0.0478	0.1881	0.0237	0.1859	0.016	-0.0272	0.2839	0.0273	0.3075	19.0163	47.3655	8.9162
5	2.7784	0.6911	0.0603	2.5474	-0.5477	2.4509	-0.1081	-0.3033	-0.1301	-0.1279	-0.1134	0.1384	-0.0975	-0.1282	0.0654	0.231	0.0297	-0.0263	0.214	0.0231	0.2412	8.917	45.1428	9.0724
6	1.6325	0.8547	0.8996	3.6853	0.4678	4.4949	-0.1996	-0.3844	0.4176	0.228	0.1026	0.851	-0.6914	-0.4303	-0.0565	0.2292	0.0059	0.0513	0.2964	-0.0181	0.2146	-6.7306	67.6251	-3.4736
7	3.1925	1.2417	-0.4939	2.9895	0.727	4.1936	0.1627	0.0528	0.2574	-0.4539	-0.1134	-0.0332	-0.0606	0.3338	-0.0323	0.2774	0.0208	0.0638	0.2055	-0.0128	0.2756	22.1661	44.7499	-11.8394
8	1.9966	-0.5683	0.2183	0.8131	0.3487	0.4092	0.0081	0.335	0.0863	-0.1528	-0.1097	-0.1072	0.0726	0.1164	0.0977	0.3019	0.0172	0.0492	0.2844	0.0583	0.2733	4.5401	45.0452	-22.374
9	2.2763	-0.9084	-1.5572	3.2178	0.5609	2.3912	0.0666	-0.0119	0.0535	0.1606	-0.2686	-0.0623	0.2242	-0.2063	0.0557	0.2931	-0.0093	-0.0509	0.22	0.0588	0.2306	49.1933	70.2132	-3.6189
10	1.8989	-1.6632	-1.1342	2.0979	0.3166	2.1417	-0.0388	0.1645	-0.3654	-0.0832	-0.1514	0.1722	0.3521	-0.3616	0.206	0.2651	-0.0997	-0.0122	0.2002	0.0494	0.2277	45.8583	62.2172	1.7058
11	1.8417	0.0409	-0.3453	2.1474	0.1002	1.9753	-0.0677	-0.0083	0.0012	-0.0347	-0.0192	0.1173	0.0726	-0.0786	0.0792	0.2267	-0.0258	-0.01	0.2093	0.004	0.1942	25.1351	82.6832	2.2525
12	1.6754	-0.4911	-0.5228	1.4269	-0.0932	0.6947	-0.2978	-0.5985	-0.0529	0.3308	0.2708	-0.154	-0.0023	0.2511	-0.0215	0.2745	0.0083	-0.0663	0.2876	0.0066	0.2505	53.8826	64.5309	5.6788
13	8.0145	-2.3752	1.2528	3.3813	0.6181	3.4751	-0.2799	0.3825	0.2237	0.1292	-0.0169	-0.124	-0.0122	0.1804	0.2434	0.2873	-0.0639	-0.0081	0.2727	-0.0281	0.1229	16.9074	12.3654	-11.21
14	2.5246	0.5289	-0.4944	6.0646	-0.955	1.9951	0.1584	0.1629	-0.019	-0.6209	-0.147	0.4431	0.1558	-0.1249	0.0262	0.2732	0.0235	-0.0261	0.281	-0.0084	0.1669	11.3193	6.4623	-13.4588
15	1.6358	0.2428	-0.8173	4.8828	0.3772	3.3021	0.5282	-0.461	0.6613	-0.2887	-0.1312	0.2767	-0.5571	-0.2572	-0.026	0.2621	0.0288	-0.0041	0.3161	0.0093	0.2878	12.1502	24.9055	-6.2013
16	4.8008	-0.6524	-0.512	1.0057	-0.5327	0.5305	0.0199	0.0711	-0.0246	0.0472	0.04	-0.1574	-0.0031	-0.0195	-0.0914	0.2216	-0.0282	0.0144	0.1097	-0.0012	0.1452	24.4082	13.9411	-2.5397
17	4.6224	1.3402	-0.831	2.2269	-1.7363	4.4582	-0.0232	-0.493	0.7259	0.2681	0.03	-0.6231	-0.0638	0.2675	-0.1373	0.2851	0.0178	-0.0981	0.4422	-0.0383	0.5343	51.1812	15.2989	-1.996
18	4.9448	-0.4289	-3.5976	2.0817	1.7709	6.663	0.5646	0.4049	0.902	-0.1627	-0.0858	-0.3529	-0.5844	-0.5807	0.073	0.1872	-0.0195	-0.05	0.2232	-0.0247	0.4749	40.3615	20.3123	-5.3553
19	1.9939	-0.1433	-0.4003	2.7307	-0.2886	1.2716	-0.0154	0.1762	0.1559	0.0512	0.1092	-0.3302	0.011	-0.0348	-0.0257	0.2572	-0.0062	-0.0104	0.2562	0.0346	0.3311	39.3427	13.3258	-8.017
20	2.2337	-0.5615	1.6915	1.511	-0.9423	1.4551	-0.2541	-0.4183	0.3432	0.0404	0.3685	-0.1012	-0.3476	0.2125	0.0297	0.2474	-0.0629	0.0143	0.2244	-0.0553	0.2237	22.4365	15.1023	1.3699
21	1.2924	1.7504	0.974	3.6093	0.0184	4.0148	0.0177	-0.7294	0.3874	-0.0295	0.2082	0.1493	0.018	-0.5102	-0.1815	0.2088	0.032	0.0164	0.2055	0.0154	0.2091	4.0897	7.3577	-3.3176
22	2.4694	0.2186	1.0555	3.1268	0.7983	1.8095	0.3189	-0.1028	-0.0522	0.1139	-0.2997	0.0731	0.0138	-0.1737	-0.0157	0.2661	0.009	0.0737	0.2414	0.0315	0.2761	38.3689	22.8122	-24.5253
23	4.173	1.5413	0.9229	0.9048	0.6738	3.6776	-0.394	0.1122	0.2256	-0.0857	-0.0038	-0.2797	-0.1547	0.0072	0.2444	0.1695	-0.0049	0.0716	0.268	0.1066	0.3225	34.3844	27.1636	-35.1033
24	1.9719	-0.6629	-0.4838	2.2986	-0.3749	2.1248	0.1225	-0.0269	-0.0347	0.096	-0.0591	0.0374	-0.1249	0.0403	-0.1124	0.1624	-0.008	-0.0222	0.203	0.0186	0.1194	16.1676	5.6693	-30.0101
25	1.2266	1.1347	0.3538	1.2196	0.4663	0.8185	-0.0776	0.3235	0.1178	-0.1629	0.1416	-0.0656	-0.0656	0.0046	-0.0323	0.2367	-0.0341	0.0667	0.3432	0.043	0.3122	39.9548	24.0271	-34.5702
26	3.8101	1.2573	-1.6287	2.9782	0.7754	2.2697	-0.0022	-0.0377	-0.1766	-0.1502	-0.041	-0.0232	-0.1173	-0.2418	0.1125	0.2731	-0.0293	-0.037	0.3483	0.063	0.2391	23.8829	80.0435	-16.6424
27	2.7667	-0.2965	-0.3438	0.1835	0.3129	0.6821	0.0391	-0.0794	-0.2118	-0.0465	-0.1936	0.0783	0.252	-0.2277	0.1336	0.3631	-0.0326	-0.0217	0.2928	-0.0508	0.2833	24.5579	72.9613	-22.6324
28	2.3584	-0.3236	0.8597	3.6669	-0.542	2.0494	0.049	0.1151	-0.0517	-0.0031	-0.0919	-0.2261	0.0531	0.1299	0.0095	0.1644	0.0027	0.0168	0.1724	0.016	0.1774	50.2668	74.116	-22.2727
29	3.0525	-0.5789	-1.77	2.2731	0.3293	2.6612	0.1911	0.391	-0.004	-0.4522	-0.0915	0.313	-0.4912	-0.398	0.042	0.3483	0.0344	-0.0669	0.302	0.0218	0.2616	18.0512	79.9081	-25.5662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 90 through 106 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 107 through 137 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 138 through 171 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 172 through 228 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 229 through 261 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 262 through 288 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 90 through 152 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 153 through 288 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 88 through 116 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 117 through 160 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 161 through 261 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 262 through 288 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 90 through 106 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 107 through 127 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 128 through 137 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 138 through 173 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 174 through 185 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 186 through 201 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 202 through 256 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 257 through 269 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 270 through 288 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 90 through 137 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 138 through 160 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 161 through 256 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 257 through 288 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 89 through 116 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 117 through 167 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 168 through 261 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 262 through 288 )

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