PDB-5fhk: Regulatory domain of AphB in Vibrio vulnificus

ID or keywords:

Entry

Database: PDB / ID: 5fhk

Title

Regulatory domain of AphB in 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: 1.905 Å

Authors

Song, S. / 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	Dec 22, 2015	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 10, 2017	Group: Database references
Revision 1.2	May 24, 2017	Group: Database references
Revision 1.3	Nov 8, 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	5fhk.cif.gz	477.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5fhk.ent.gz	396.4 KB	Display	PDB format
PDBx/mmJSON format	5fhk.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/fh/5fhk ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fhk	HTTPS FTP

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Related structure data

Related structure data	5x0nC 5x0oC 3szpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5x0o-1 5x0n-2 5x0n-1 1551 5x0n-3 2xqq-d 3ouq-2 3gl1-1 5x0o-3 2pz9-1 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

5x0nC

5x0oC

3szpS

S: Starting model for refinement

C: citing same article (ref.)

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)	124.965, 187.926, 57.360
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-HA / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A087IWB4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H₂O

#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-HA / Production host:

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

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H₂O

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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: 48.71 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES:NaOH (pH 7.5), 15% PEG 8000, 10% Ethylene glycol PH range: 7.0-8.0 / Temp details: melting at 295K

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Data collection

Diffraction	Mean temperature: 200 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	Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 1.9→42.26 Å / Num. obs: 90980 / % possible obs: 98.1 % / Redundancy: 8.7 % / B_iso Wilson estimate: 19.4 Å² / R_merge(I) obs: 0.111 / Net I/σ(I): 14.08
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.639 / Mean I/σ(I) obs: 3.73 / % possible all: 85.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.11_2567: ???)	refinement
HKL-2000		data processing
HKL-2000		data scaling
PHENIX		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SZP

3szp

Resolution: 1.905→42.255 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 24.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2507	4544	4.99 %
R_work	0.208	-	-
obs	0.2101	90978	85.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.905→42.255 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9465	0	0	301	9766

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	9709
X-RAY DIFFRACTION	f_angle_d	1.021	13187
X-RAY DIFFRACTION	f_dihedral_angle_d	2.788	7075
X-RAY DIFFRACTION	f_chiral_restr	0.062	1486
X-RAY DIFFRACTION	f_plane_restr	0.007	1684

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 (%)
1.9054-1.927	0.666	3	0.4068	178	X-RAY DIFFRACTION	5
1.927-1.9497	0.279	21	0.2534	385	X-RAY DIFFRACTION	12
1.9497-1.9735	0.2579	50	0.2372	961	X-RAY DIFFRACTION	29
1.9735-1.9984	0.2826	99	0.2394	1613	X-RAY DIFFRACTION	49
1.9984-2.0247	0.2974	123	0.2406	2167	X-RAY DIFFRACTION	65
2.0247-2.0525	0.2791	123	0.2367	2560	X-RAY DIFFRACTION	76
2.0525-2.0818	0.2907	158	0.2375	2819	X-RAY DIFFRACTION	86
2.0818-2.1129	0.2948	158	0.2494	2988	X-RAY DIFFRACTION	89
2.1129-2.1459	0.2772	167	0.2609	3117	X-RAY DIFFRACTION	94
2.1459-2.1811	0.2531	171	0.2498	3224	X-RAY DIFFRACTION	96
2.1811-2.2187	0.2724	177	0.2465	3155	X-RAY DIFFRACTION	95
2.2187-2.259	0.5093	147	0.347	2831	X-RAY DIFFRACTION	85
2.259-2.3025	0.3147	172	0.2417	2893	X-RAY DIFFRACTION	86
2.3025-2.3495	0.289	153	0.2176	3313	X-RAY DIFFRACTION	99
2.3495-2.4005	0.2568	160	0.2186	3339	X-RAY DIFFRACTION	99
2.4005-2.4564	0.252	201	0.2221	3271	X-RAY DIFFRACTION	99
2.4564-2.5178	0.2788	189	0.2253	3329	X-RAY DIFFRACTION	99
2.5178-2.5859	0.256	159	0.2242	3372	X-RAY DIFFRACTION	100
2.5859-2.6619	0.2889	179	0.2212	3321	X-RAY DIFFRACTION	100
2.6619-2.7478	0.2984	169	0.2217	3379	X-RAY DIFFRACTION	100
2.7478-2.846	0.2346	164	0.2161	3364	X-RAY DIFFRACTION	100
2.846-2.96	0.2236	168	0.2086	3342	X-RAY DIFFRACTION	100
2.96-3.0946	0.2599	184	0.2136	3373	X-RAY DIFFRACTION	100
3.0946-3.2577	0.2461	172	0.2077	3393	X-RAY DIFFRACTION	100
3.2577-3.4617	0.2344	184	0.198	3378	X-RAY DIFFRACTION	100
3.4617-3.7289	0.2386	165	0.1912	3419	X-RAY DIFFRACTION	100
3.7289-4.1039	0.2273	193	0.1742	3415	X-RAY DIFFRACTION	100
4.1039-4.697	0.1918	163	0.1515	3446	X-RAY DIFFRACTION	100
4.697-5.9152	0.2001	188	0.168	3484	X-RAY DIFFRACTION	100
5.9152-42.2651	0.1979	184	0.1858	3605	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	1.6034	0.0645	0.6494	0.6451	0.5165	1.4143	-0.1617	0.0154	0.3413	-0.1697	-0.2344	-0.2742	0.0226	0.2029	0.2352	0.1321	0.0222	0.0139	0.1606	0.113	0.2937	-2.8294	58.9826	-9.6306
2	1.2368	-0.2138	-0.6917	0.6824	-0.5541	1.1095	-0.0812	0.0019	0.5872	0.2852	-0.2068	-0.4394	-0.4911	0.3855	-0.0916	0.2426	-0.096	-0.1284	0.1722	0.1623	0.6753	4.6304	68.5815	-1.6243
3	1.4746	0.2664	-0.7174	1.7921	0.4122	1.9281	-0.058	-0.1424	0.0171	0.1083	-0.039	-0.1586	-0.1039	0.2855	0.0834	0.2039	-0.0026	-0.0065	0.1949	0.0684	0.253	15.3639	45.9894	9.3532
4	0.5713	0.3663	0.7761	0.9392	0.1446	1.307	-0.2355	-0.1831	0.5431	0.0756	-0.1346	-0.0348	-0.0858	-0.2296	0.0402	0.173	0.0272	-0.0467	0.1382	0.0077	0.4568	-6.3397	67.3077	-3.3991
5	1.5372	0.2638	-0.2142	1.1975	0.185	2.1377	-0.0437	0.1261	-0.0001	-0.2241	0.0353	-0.181	-0.2607	0.1681	0.0109	0.3047	0.0173	0.1168	0.2403	0.0447	0.3878	22.4918	44.6958	-11.9164
6	1.7856	-0.2269	0.1977	0.308	0.0284	0.0287	0.5946	0.4895	-0.1414	-0.2627	-0.4029	-0.1629	0.0456	0.0293	0.0728	0.303	0.0858	0.1024	0.2353	0.021	0.2443	3.0938	41.3675	-21.8498
7	0.7929	0.1302	-0.3187	0.8808	0.1187	0.6404	0.1257	0.7242	0.1403	-0.5709	-0.1356	-0.071	-0.0382	0.3138	-0.3033	0.3605	0.1722	0.1002	0.6204	0.2383	0.1997	-2.9586	50.7726	-29.0831
8	1.0008	-0.0852	0.7713	0.4957	-0.0465	0.7568	0.1117	0.4979	0.012	-0.1367	-0.2524	-0.2939	0.574	0.646	-0.1674	0.3726	0.2862	0.1387	0.2741	0.1011	0.1993	-0.8637	44.202	-19.3519
9	1.2845	-0.1199	0.3198	2.12	-0.3234	2.0864	-0.096	0.2525	-0.286	-0.2313	0.0592	-0.166	0.2991	0.5111	0.069	0.35	0.0466	0.1803	0.29	0.0291	0.4445	28.3364	38.1072	-15.8845
10	2.0697	-0.0727	-0.4707	1.7244	0.2228	1.8594	0.0041	-0.0825	-0.2694	0.0991	-0.0715	0.0995	-0.0005	-0.1256	0.0399	0.1706	-0.0115	-0.0414	0.1126	0.0378	0.1763	48.7242	64.6631	-2.6114
11	1.0145	-0.6528	-0.1982	0.6608	0.1113	0.0302	0.0073	-0.054	-0.004	0.0215	-0.0043	0.0047	0.0954	-0.0189	-0.0085	0.1645	-0.0125	-0.0077	0.1239	0.0078	0.091	32.7495	77.0881	2.6787
12	1.2948	0.0539	0.3118	1.6357	-0.0388	1.5552	0.0155	0.109	0.154	-0.0389	0.0133	-0.0104	-0.1424	0.0117	0.0015	0.1037	-0.005	0.0167	0.1032	0.0107	0.0764	13.2494	13.4324	-6.9378
13	1.6637	0.6076	-0.4957	1.5796	0.404	1.8596	0.1621	-0.0851	0.2657	0.1697	-0.0207	-0.5093	0.0152	0.0304	-0.0577	0.0918	-0.023	0.0092	0.1713	0.0196	0.2775	44.528	15.1419	-3.0625
14	1.0237	0.2959	-0.1551	0.937	0.1736	0.6187	0.012	0.0345	0.0636	-0.0581	0.0207	-0.1168	0.0243	0.0005	-0.0345	0.1339	-0.0239	-0.0026	0.1317	0.0099	0.1834	39.0438	13.1994	-7.6159
15	0.8481	0.9992	0.4313	1.7372	0.362	1.2631	0.0167	-0.2822	0.2319	0.1897	-0.0643	0.3168	0.0238	-0.1471	0.0121	0.0966	-0.0132	0.0277	0.103	-0.0223	0.1127	7.9813	9.4265	-1.5002
16	1.2823	-0.347	0.3704	1.5723	0.0485	1.2458	0.1164	0.0773	0.2336	-0.1163	-0.059	-0.0154	-0.0561	-0.0602	-0.0249	0.2079	-0.0341	0.0971	0.2	0.0362	0.2721	39.0009	22.657	-23.898
17	1.8576	0.7208	-0.3891	2.0185	1.1092	1.4231	-0.0355	0.3596	0.2059	-0.5985	-0.0102	0.0664	-0.3363	-0.251	-0.0512	0.2797	-0.0871	0.1287	0.2482	0.0879	0.2282	34.9356	27.0727	-35.0806
18	0.9111	0.3366	-0.493	1.2825	-0.0906	1.6345	0.0914	-0.0026	0.0328	0.0437	-0.0238	-0.003	-0.0948	0.0862	-0.0491	0.089	0.0024	0.0062	0.1288	0.0108	0.0575	16.272	5.683	-29.4545
19	0.4583	0.3821	0.2401	0.651	0.2033	0.3003	-0.1462	0.3864	0.1894	-0.3892	0.1882	-0.1243	-0.0998	0.1558	-0.1224	0.1782	-0.0662	0.1023	0.2662	0.0486	0.2631	40.3665	23.7891	-34.045
20	1.5338	0.2294	-0.1998	1.8126	0.0439	1.5795	-0.1023	0.0617	-0.1466	-0.0197	0.1122	0.0032	0.2511	-0.0496	-0.0083	0.2113	-0.0303	-0.0208	0.2006	0.0216	0.1382	22.3098	75.6885	-17.6704
21	1.8048	-0.0753	0.4243	0.6366	-0.4678	0.7815	0.1081	0.2331	-0.0441	-0.0543	-0.1041	-0.0702	0.1213	0.0771	-0.0065	0.1865	-0.0031	0.0188	0.1493	-0.0341	0.1109	42.9112	72.6812	-25.1108
22	1.3047	-0.1516	0.2528	1.8476	-0.6267	0.8326	0.0879	0.137	-0.0675	-0.0518	-0.1038	0.0335	0.0987	-0.0327	0.0181	0.1134	0.0028	0.0024	0.1337	-0.0113	0.1138	47.9963	73.8699	-22.9983
23	1.117	-1.4117	-0.6428	1.8123	0.6602	1.6069	0.1765	0.5172	-0.1619	-0.0918	-0.1554	0.2492	0.0647	-0.4402	-0.0727	0.1798	-0.046	-0.0351	0.3609	0.029	0.16	17.0202	78.4282	-27.1005

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 90 through 127 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 128 through 161 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 162 through 261 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 262 through 289 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 91 through 152 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 153 through 173 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 174 through 214 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 215 through 261 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 262 through 288 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 87 through 152 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 153 through 288 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 87 through 160 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 161 through 205 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 206 through 261 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 262 through 289 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 89 through 137 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 138 through 160 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 161 through 256 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 257 through 288 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 89 through 137 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 138 through 196 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 197 through 261 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 262 through 289 )

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