PDB-6wai: Crystal Structure of SmcR N142D from Vibrio vulnificus

ID or keywords:

Entry

Database: PDB / ID: 6wai

Title

Crystal Structure of SmcR N142D from Vibrio vulnificus

Components

LuxR family transcriptional regulator

Keywords

TRANSCRIPTION / quorum-sensing / transcription factor / DNA-binding protein

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.583 Å

Authors

Newman, J.D. / Russell, M.M. / Gonzalez-Gutierrez, G. / van Kessel, J.C.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2021
Title: The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.
Authors: Newman, J.D. / Russell, M.M. / Fan, L. / Wang, Y.X. / Gonzalez-Gutierrez, G. / van Kessel, J.C.

History

Deposition	Mar 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 30, 2021	Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2	Oct 18, 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	6wai.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6wai.ent.gz	281.5 KB	Display	PDB format
PDBx/mmJSON format	6wai.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wai_validation.pdf.gz	502.8 KB	Display	wwPDB validaton report
Full document	6wai_full_validation.pdf.gz	537.2 KB	Display
Data in XML	6wai_validation.xml.gz	34.8 KB	Display
Data in CIF	6wai_validation.cif.gz	46.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wa/6wai ftp://data.pdbj.org/pub/pdb/validation_reports/wa/6wai	HTTPS FTP

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Related structure data

Related structure data	6waeC 6wafC 6wagC 6wahC 3kz9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6wag-1 3kz9-2 6wag-2 5x3r-2 6wah-2 6wah-1 5x3r-1 5d1w-3 6wae-2 6wae-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) 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

Deposited unit

A: LuxR family transcriptional regulator

B: LuxR family transcriptional regulator

C: LuxR family transcriptional regulator

D: LuxR family transcriptional regulator

hetero molecules

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

1

A: LuxR family transcriptional regulator

B: LuxR family transcriptional regulator

hetero molecules

defined by author&software
Evidence: gel filtration
51.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: LuxR family transcriptional regulator

D: LuxR family transcriptional regulator

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.021, 99.565, 129.469
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	LuxR family transcriptional regulator / SmcR / SmcR-like protein / TetR/AcrR family transcriptional regulator / VvpR Mass: 25918.350 Da / Num. of mol.: 4 / Mutation: N142D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) Gene: smcR, vvpR, CRN32_08135, CRN52_17705, D8T54_02235, D8T65_23975, JS86_16400 Production host: Escherichia coli (E. coli) / References: UniProt: Q9L8G8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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.: 115 / 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: 2.43 Å³/Da / Density % sol: 49.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M of Lithium Sulfate, 0.1 M Imidazole buffer pH 7.6-8 and 6-10% PEG3350 PH range: 7.6 - 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9763 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 16, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.58→78.92 Å / Num. obs: 32305 / % possible obs: 99.99 % / Redundancy: 7.1 % / CC_1/2: 0.998 / R_pim(I) all: 0.067 / R_rim(I) all: 0.179 / R_sym value: 0.166 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.58→2.66 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1592 / CC_1/2: 0.626 / R_pim(I) all: 0.673 / R_rim(I) all: 1.759 / R_sym value: 1.623 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.15_3459: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3kz9

3kz9

Resolution: 2.583→78.92 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 31.2

	R_factor	Num. reflection	% reflection
R_free	0.286	1666	5.18 %
R_work	0.2313	-	-
obs	0.234	32181	99.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.583→78.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6521	0	13	115	6649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6660
X-RAY DIFFRACTION	f_angle_d	0.662	9032
X-RAY DIFFRACTION	f_dihedral_angle_d	1.926	3126
X-RAY DIFFRACTION	f_chiral_restr	0.043	1022
X-RAY DIFFRACTION	f_plane_restr	0.004	1173

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 (%)
2.5833-2.6594	0.381	140	0.3266	2453	X-RAY DIFFRACTION	99
2.6594-2.7452	0.3404	135	0.3066	2517	X-RAY DIFFRACTION	99
2.7452-2.8433	0.3436	151	0.2914	2482	X-RAY DIFFRACTION	100
2.8433-2.9572	0.3107	140	0.2778	2508	X-RAY DIFFRACTION	100
2.9572-3.0918	0.3166	134	0.2611	2534	X-RAY DIFFRACTION	100
3.0918-3.2548	0.2988	116	0.2513	2538	X-RAY DIFFRACTION	100
3.2548-3.4587	0.3027	134	0.2375	2526	X-RAY DIFFRACTION	100
3.4587-3.7257	0.2949	158	0.2245	2530	X-RAY DIFFRACTION	100
3.7257-4.1007	0.2789	129	0.2013	2566	X-RAY DIFFRACTION	100
4.1007-4.694	0.2423	147	0.1915	2536	X-RAY DIFFRACTION	100
4.694-5.9136	0.2609	142	0.2215	2614	X-RAY DIFFRACTION	100
5.9136-78.925	0.2563	140	0.2036	2711	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	3.8246	4.0367	0.8314	4.9827	-0.3347	2.9418	0.3809	-0.3344	0.1599	0.3054	-0.5766	-0.2235	-0.4486	0.8308	0.3167	0.5838	-0.0241	-0.0476	0.7808	-0.0637	0.6214	33.8453	24.2384	-1.3137
2	3.3773	0.5542	0.0417	1.9001	0.666	3.1001	-0.0543	-0.1495	0.2385	0.131	0.0595	0.0213	-0.2897	-0.1375	0.0069	0.3392	0.1023	-0.0231	0.437	-0.0805	0.3586	17.2522	8.6408	-12.938
3	2.2921	1.7152	2.5913	3.6282	-0.1197	4.6961	0.1642	-0.2297	0.4189	0.1412	-0.5261	-0.8124	-0.2467	1.0696	0.2861	0.5244	0.0418	0.0365	1.0316	0.2158	0.6461	59.2395	-2.9016	-11.3375
4	6.2581	-0.3096	-0.7547	3.4242	-1.1446	3.5196	-0.1992	-0.0636	-0.2828	0.3791	0.3038	-0.2785	0.359	-0.0269	-0.0932	0.3774	-0.0983	-0.0526	0.5344	-0.0336	0.4531	52.8843	-0.1284	-18.0258
5	6.1009	0.8496	0.1574	2.0695	-0.3179	1.2162	0.07	-0.3342	0.626	0.103	-0.287	-0.0164	-0.1265	0.3743	0.2061	0.4475	-0.0579	0.0762	0.5803	-0.0193	0.3471	50.559	3.9485	-21.7607
6	6.4543	-0.7717	0.1473	2.7842	0.1098	1.8963	0.424	0.6214	-1.1828	-0.4277	0.1944	0.0821	0.3653	0.1359	-0.4731	0.4427	0.0131	0.0039	0.282	0.0334	0.4517	27.5258	-10.2879	-24.3271
7	4.5236	0.5331	-0.3308	0.7616	0.4715	2.4944	-0.1467	0.5723	0.2762	-0.2316	0.1576	0.0561	-0.036	0.6737	-0.0183	0.3743	0.0415	0.0139	0.7565	0.0306	0.3399	34.0277	3.5843	-26.1363
8	3.9868	-0.225	2.0892	2.7649	-1.3511	5.5501	0.2573	0.558	-0.5254	-0.0214	-0.1188	-0.003	0.1708	0.6787	-0.0628	0.3	0.0703	-0.0004	0.4526	0.0248	0.3528	22.8053	0.8005	-24.8529
9	3.3878	-1.4445	-0.7007	0.9426	-0.0149	5.4207	0.5043	-1.442	-0.4186	-0.0981	0.2303	0.1565	0.4492	-0.159	-0.1215	0.4862	-0.0501	-0.0085	0.3997	-0.0977	0.4064	23.549	-7.7827	-12.054
10	8.5303	0.2891	0.6775	4.8165	3.1797	4.4996	-0.5423	0.0506	-0.3432	-2.7348	0.2046	0.807	-0.0728	-0.1798	0.3526	0.7907	-0.0998	-0.0283	0.3527	-0.0638	0.4156	12.3737	-8.5627	-28.6682
11	6.1258	0.715	0.87	4.5702	0.2505	0.9102	0.0278	0.157	0.7832	-1.2768	0.5479	-0.0146	1.1697	-0.6416	0.0625	0.9462	-0.1133	-0.1434	0.4552	-0.0297	0.555	20.4465	-15.8918	-2.1671
12	1.6324	1.0612	1.5545	5.022	1.7283	3.2614	0.4842	0.0033	0.2507	-0.4527	-0.3163	-0.0311	-0.6046	-0.4532	0.1081	0.3665	-0.0623	-0.0315	0.4966	-0.1597	0.4428	15.8589	-24.5705	-1.4398
13	2.3334	2.1833	0.7793	3.1261	1.2021	2.3189	0.4189	0.091	-0.897	0.2414	0.4061	-1.0887	-0.1392	0.2634	-0.6823	0.5017	-0.1275	-0.0795	0.7105	-0.1679	0.6853	22.9528	-26.6565	2.7419
14	7.0359	1.2712	3.4055	2.9966	0.9759	4.4906	0.1967	-2.1116	0.6333	0.2502	0.008	-0.4356	-0.2239	-0.5938	-0.1846	0.4872	-0.0704	0.0212	0.5523	-0.2898	0.5572	6.597	-33.7715	0.0139
15	3.5536	0.8671	2.1029	2.5492	1.4889	3.3697	-0.0866	0.0423	0.5995	-0.1826	-0.0027	0.0549	-0.4498	0.2908	0.0648	0.4196	-0.0027	0.0378	0.369	-0.0185	0.3439	-0.2051	-35.1187	-11.9486
16	7.1687	2.5112	-0.2263	2.4908	3.735	9.9719	0.1584	-0.954	0.2885	-0.469	-0.4541	-2.3266	-1.3383	2.2823	0.3963	0.5905	-0.1436	-0.0605	0.736	-0.0018	0.8921	18.5448	-46.2882	-3.7023
17	5.8293	0.7553	2.0005	2.6051	0.2434	2.7947	0.3141	-1.0202	0.4087	0.3287	-0.2276	0.1798	0.2747	-0.025	-0.0913	0.3785	-0.0662	0.0138	0.5267	-0.0825	0.2881	-1.3679	-45.5037	-2.161
18	4.9347	-0.8895	2.0303	4.2249	-2.4629	4.9339	-0.5627	0.952	-0.5401	0.3443	0.6002	0.0714	-0.2038	-0.4887	-0.2324	0.4918	-0.0228	0.1036	0.3772	-0.0247	0.4651	-12.5913	-52.605	-11.0687
19	5.2578	2.9915	-3.5966	4.3328	-4.5449	7.1833	0.1751	-0.5158	-0.2361	0.2206	-0.5857	-0.3814	-0.3234	1.0392	0.3202	0.3389	0.0096	-0.0198	0.2482	-0.0518	0.2753	3.8231	-43.2936	-14.8305
20	3.769	-1.8543	-0.288	4.0545	-0.9386	5.2055	-0.3989	0.4687	1.2126	-0.3954	0.6271	-0.181	-0.4905	-0.3035	-0.1406	0.4638	0.0564	-0.0551	0.5105	-0.0108	0.566	-0.0339	-37.1617	-25.7138
21	1.6425	-1.1109	0.4743	2.5523	0.0585	0.2016	-0.1968	-0.1046	-0.1968	1.4312	0.3979	1.1422	0.0399	-1.9687	0.1609	0.5185	0.0789	0.097	1.397	-0.0453	0.597	-17.0676	-50.2905	-17.3661
22	2.7057	3.4559	1.6775	6.1475	-0.8064	6.1966	1.386	0.5878	0.179	0.6559	-0.2836	-2.1768	-0.5627	0.744	-0.8055	0.964	0.118	0.3099	0.8212	0.0456	0.9759	44.0363	-56.2006	-14.3245
23	5.5285	-1.8275	-0.9634	3.0662	0.8594	2.8909	-0.4796	-1.2998	0.3202	0.086	1.1091	-0.0961	-0.0458	1.1311	-0.5265	0.5471	-0.1079	-0.0747	1.1683	-0.1026	0.6213	34.5227	-48.8654	-15.5186
24	5.2064	0.8311	1.1833	1.2402	0.8435	2.4163	0.0017	0.4746	0.3442	0.081	0.3732	-0.2635	-0.0977	1.1538	-0.3913	0.3904	-0.0079	0.0704	0.9891	-0.1211	0.5044	31.2078	-47.8694	-23.5669
25	4.1888	-0.4424	-0.2523	2.1181	-1.0725	2.4626	0.1655	-0.5276	-0.9678	0.0051	0.0669	-0.0403	0.9717	0.1656	-0.0944	0.3899	0.0317	0.0923	0.4675	-0.1068	0.453	8.6076	-60.8722	-23.9859
26	6.186	-3.1253	1.7044	5.2353	0.7167	4.6211	-0.1781	-1.2759	-0.1432	0.7752	0.3685	-0.4913	0.343	0.396	-0.3722	0.3732	-0.0193	0.0723	0.9521	-0.0395	0.4321	20.8808	-51.2745	-17.6543
27	4.2968	1.2568	-2.1323	4.2272	-3.2136	7.9188	-1.0095	-1.2196	0.8928	-0.4227	0.6906	-2.5384	-0.6606	0.9592	0.6964	0.7424	0.0223	0.0019	0.9748	0.0542	0.7585	19.0259	-35.3435	-19.5384
28	3.7256	0.3306	0.1544	0.7481	-0.3544	2.2078	0.2332	0.3279	-0.0087	-0.0339	-0.2787	-0.1946	0.1702	0.5002	-0.0022	0.4649	0.0101	-0.011	0.5956	0.0048	0.3929	11.0454	-48.0279	-32.1041
29	3.8941	-0.9598	2.4956	2.6613	-0.1216	5.7403	-0.0425	0.1986	-0.2443	-0.2168	0.0806	-0.0135	-0.0572	0.4431	0.0626	0.3041	-0.0032	0.0387	0.3272	0.0227	0.2891	5.0703	-49.3088	-22.9108
30	4.3762	-0.2512	-1.5308	6.4434	-1.3707	2.4814	-0.2472	-0.759	-0.535	-0.2931	0.0091	-0.1663	0.2231	-0.2948	0.2364	0.3528	-0.0576	0.0954	0.4781	-0.0147	0.4196	0.7846	-58.9708	-17.682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 82 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 205 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 2 through 13 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 14 through 32 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 33 through 82 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 83 through 105 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 106 through 149 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 150 through 178 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 179 through 196 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 197 through 203 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 13 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 14 through 32 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 33 through 59 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 60 through 82 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 83 through 119 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 120 through 125 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 126 through 149 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 150 through 158 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 159 through 179 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 180 through 196 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 197 through 205 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 5 through 13 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 14 through 46 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 47 through 82 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 83 through 105 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 106 through 118 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 119 through 125 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 126 through 150 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 151 through 179 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 180 through 203 )

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