PDB-5hso: Crystal structure of MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTE...

ID or keywords:

Entry

Database: PDB / ID: 5hso

Title

Crystal structure of MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTEIN Rv2887 complex with DNA

Components

(DNA (30-MER), the upstream sequence of Rv0560c) x 2
Uncharacterized HTH-type transcriptional regulator Rv2887

Keywords

TRANSCRIPTION / HTH-TYPE TRANSCRIPTIONAL REGULATOR / DNA BINDING / SALICYLIC ACID BINDING

Function / homology

Function and homology information

response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Gao, Y.R. / Li, D.F. / Wang, D.C. / Bi, L.J.

Citation

Journal: Sci Rep / Year: 2017
Title: Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis
Authors: Gao, Y.R. / Li, D.F. / Fleming, J. / Zhou, Y.F. / Liu, Y. / Deng, J.Y. / Zhou, L. / Zhou, J. / Zhu, G.F. / Zhang, X.E. / Wang, D.C. / Bi, L.J.

History

Deposition	Jan 26, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	5hsmC 5x7zC 5x80C C: citing same article (ref.)
Similar structure data	6ka9-d 6kai-d 1j41-d 7a4d-d 6kae-d 4mqk-d 1gqm-d 6lcw-d 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Uncharacterized HTH-type transcriptional regulator Rv2887

B: Uncharacterized HTH-type transcriptional regulator Rv2887

C: Uncharacterized HTH-type transcriptional regulator Rv2887

D: Uncharacterized HTH-type transcriptional regulator Rv2887

E: DNA (30-MER), the upstream sequence of Rv0560c

F: DNA (30-MER), the upstream sequence of Rv0560c

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	48.218, 48.233, 101.115
Angle α, β, γ (deg.)	89.95, 90.04, 107.13
Int Tables number	1
Space group name H-M	P1

#1: Protein	Uncharacterized HTH-type transcriptional regulator Rv2887 Mass: 17012.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv2887, MTCY274.18 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WME9
#2: DNA chain	DNA (30-MER), the upstream sequence of Rv0560c Mass: 9265.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: DNA chain	DNA (30-MER), the upstream sequence of Rv0560c Mass: 9185.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.66 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M Potassium chloride, 0.025 M Magnesium chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, and 15% V/V 2-Propanol PH range: 7.0-7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2015
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.5→36.21 Å / Num. obs: 30122 / % possible obs: 99.8 % / Redundancy: 6.8 % / B_iso Wilson estimate: 63.2 Å² / R_merge(I) obs: 0.042 / R_sym value: 0.042 / Net I/σ(I): 15.4
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 7 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	dev_1980	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→36.21 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 34.22 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2776	1439	4.87 %	Random selection
R_work	0.2395	-	-	-
obs	0.2414	29539	98.09 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 89 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→36.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3666	1230	0	0	4896

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5089
X-RAY DIFFRACTION	f_angle_d	0.924	7140
X-RAY DIFFRACTION	f_dihedral_angle_d	21.373	2015
X-RAY DIFFRACTION	f_chiral_restr	0.034	848
X-RAY DIFFRACTION	f_plane_restr	0.005	706

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 (%)
2.5-2.5893	0.4135	156	0.3505	2790	X-RAY DIFFRACTION	98
2.5893-2.693	0.3527	136	0.3111	2823	X-RAY DIFFRACTION	98
2.693-2.8155	0.3979	110	0.3143	2835	X-RAY DIFFRACTION	98
2.8155-2.9639	0.2916	155	0.3267	2793	X-RAY DIFFRACTION	98
2.9639-3.1495	0.3321	135	0.3264	2845	X-RAY DIFFRACTION	98
3.1495-3.3925	0.3483	178	0.2932	2785	X-RAY DIFFRACTION	98
3.3925-3.7336	0.2948	157	0.2588	2844	X-RAY DIFFRACTION	99
3.7336-4.2731	0.2396	94	0.228	2836	X-RAY DIFFRACTION	99
4.2731-5.3808	0.2667	168	0.2267	2823	X-RAY DIFFRACTION	99
5.3808-36.2166	0.2373	150	0.1824	2726	X-RAY DIFFRACTION	96

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	1.6021	-2.0634	0.6397	3.3742	-0.8749	0.2426	0.6521	0.3784	0.5585	-1.208	-0.4877	0.3693	0.5949	0.0345	0.0266	0.7884	-0.0386	0.1828	0.6869	-0.041	0.9956	36.8979	39.649	122.1372
2	4.114	0.1764	0.7031	3.0874	-3.7633	3.5199	-0.3543	-1.8556	-0.6606	0.7886	1.0627	0.4362	0.6727	-0.7094	0.0384	0.9582	0.0456	-0.013	1.0868	-0.0958	0.7248	37.0094	26.0076	140.2148
3	1.4677	0.3798	-1.2998	1.4339	0.8994	1.4194	-0.2261	-0.3992	0.7977	-0.27	0.0083	-2.0431	0.089	0.1955	0.0007	0.7491	0.0721	0.1167	0.8505	-0.3099	1.2536	48.8441	33.8387	130.7484
4	1.7498	-0.3203	-0.2813	0.5494	-0.7663	1.4348	-0.5233	-2.3616	-1.4015	1.1168	-0.1398	0.2703	0.1911	1.4589	-0.0529	0.7375	-0.0091	0.2537	0.8457	0.0737	1.0456	43.8843	52.2621	130.5847
5	2.4949	-2.7297	3.0187	5.0333	-1.6454	2.845	-0.2643	-2.8084	-0.2842	0.397	0.7359	-0.638	-0.0564	-0.8734	0.0953	0.6182	-0.0617	0.1453	0.6528	-0.142	0.8677	28.421	45.8929	131.9137
6	1.6399	-0.6507	1.671	1.8266	-0.5319	0.882	0.6016	1.1443	0.7474	-1.168	-0.1299	-0.02	0.5745	-0.3106	0.0092	0.8961	0.0301	0.1874	0.8806	0.1551	0.6057	17.6773	46.0955	115.0749
7	1.1101	0.7125	1.3872	2.2624	0.3449	2.7843	1.1284	1.1481	-0.3453	-0.8255	-0.2498	0.4638	0.5599	-0.0621	0.0042	1.2429	0.0423	-0.0047	1.1931	0.062	0.8511	13.9854	39.5176	112.9409
8	0.8243	0.7667	-0.091	0.4068	0.7799	0.9749	0.3482	-0.583	1.9126	-0.2337	-0.2617	-0.0205	0.0798	-0.5745	0.0805	0.7791	0.0624	0.3174	0.7902	-0.0484	1.2172	19.3434	55.6022	123.2728
9	4.3459	-4.2769	-4.1202	6.6665	7.2566	9.7273	0.2629	1.5806	-0.8901	-2.3923	-0.9784	0.6292	-1.4948	-1.0228	-0.2045	0.6318	0.0271	0.0131	0.6309	-0.2845	1.0191	38.2979	56.237	123.5316
10	8.9991	-0.8659	-1.4205	5.4407	0.4034	1.8758	0.5328	0.5744	0.169	-0.9266	-0.0498	0.073	-0.5345	0.4088	0.0015	0.7653	-0.048	-0.1664	0.6942	-0.0129	0.6027	15.2069	2.8568	70.2551
11	4.2797	1.306	0.8765	1.9652	-0.6136	0.7921	1.6351	-0.7466	1.1094	-1.663	-1.8994	-1.0587	0.2695	2.7904	0.0531	1.2537	0.1267	0.1104	1.5649	-0.3989	0.8502	26.5423	1.726	57.4952
12	3.0331	1.5947	-3.6282	0.475	1.7126	1.0827	0.1594	0.1692	-0.0013	-0.0694	0.1877	0.1431	0.5084	0.3639	-0	0.7383	0.0681	-0.1826	0.7684	0.1579	0.8984	8.0111	-10.1837	72.8364
13	2.2782	-0.0275	-0.7068	3.3397	0.2835	0.8849	0.677	0.5465	-0.1134	-1.8053	-0.5111	-1.1366	-0.6038	-0.0285	0.0277	0.7261	-0.0194	-0.1377	0.5785	0.0903	0.827	-0.8765	6.1406	71.5537
14	3.5174	0.3786	0.2688	2.1452	1.9606	2.7418	-0.2071	-1.6177	0.2423	0.928	0.9432	0.0945	-0.6308	0.6509	0.0161	1.0165	0.03	0.0686	1.1192	0.0802	0.7265	-0.9607	19.7141	89.6913
15	0.951	-0.2396	1.2949	1.5001	1.0659	1.1375	-0.2635	-0.2231	-0.6282	-0.6575	-0.1281	2.2726	-0.1718	-0.1894	-0.0092	0.7857	0.0665	-0.0559	0.8693	0.2617	1.1085	-12.9058	11.8659	80.1286
16	0.4849	-0.1448	0.03	0.2297	-0.1493	0.4962	-0.0136	-2.225	0.444	1.0551	-0.3173	-1.2471	-0.2238	-1.1545	-0.0062	0.698	-0.0407	-0.2646	0.8087	-0.0315	1.0057	-10.2195	-6.6441	77.9399
17	0.6001	0.1047	-0.2072	0.0056	-0.0028	0.131	-1.4706	-1.9405	0.278	2.082	-0.568	2.9713	-1.6344	-0.6456	-0.0121	1.1377	0.1053	0.0687	1.2895	-0.0302	1.2817	-0.0801	-5.8157	86.3528
18	0.0557	0.4814	-0.0122	0.5401	0.5072	-0.0917	-0.3672	0.0631	0.4837	0.2128	0.5846	-0.3567	1.7813	0.6113	-0.0012	1.844	0.1111	0.1293	1.995	-0.0573	0.8328	21.8457	22.5235	59.2517
19	2.1046	-0.6562	1.7376	1.3894	0.1013	1.1671	-1.2396	0.8154	-1.7176	-0.8886	0.4904	0.5179	1.2355	-1.6034	-0.0723	1.2079	-0.3477	0.2062	0.9717	-0.1881	0.8474	16.1625	26.8323	75.9553
20	1.885	-2.2651	1.2317	4.8237	1.4849	5.7771	-0.9348	-0.7669	-0.8101	-0.9908	0.0076	-2.2677	2.6239	3.3137	-1.5842	1.7218	-0.4208	0.6656	2.0129	0.1812	1.3175	22.8846	22.3111	93.4473
21	0.0065	0.1105	0.1446	0.3307	-0.6825	0.0107	-0.1336	1.5343	-0.1523	-0.9697	0.6025	0.382	-1.3005	-1.1195	0.0027	1.9328	0.1757	-0.026	1.964	0.165	0.9308	14.2837	23.1121	109.8577
22	3.6035	-2.3134	-0.8522	2.3233	0.2381	0.2272	-0.531	-0.3829	3.0405	0.1448	1.5791	-2.6138	-0.8093	0.8873	0.0284	1.0606	-0.33	0.0957	1.098	0.1587	0.557	19.9697	18.7992	126.4671
23	1.92	0.1643	-0.5613	0.492	-0.3858	1.0535	-0.4906	-1.1565	1.3137	0.1874	-0.6077	1.5894	-2.2202	-0.7883	-1.8437	1.8257	-0.3742	-0.2437	2.1125	-0.3295	1.2818	13.2414	23.5882	143.8084
24	0.4198	0.9288	-1.3876	1.9537	-0.1834	2.1861	-0.2875	-0.3885	0.5629	0.0828	-0.5252	-1.0658	-0.1638	2.2737	-0.147	1.5056	-0.0676	-0.1401	1.5782	0.2191	1.0014	17.7006	20.4975	127.4188
25	0.8265	0.2581	-0.3595	0.289	-0.095	-0.0653	-0.3218	0.5503	-0.6774	1.3176	1.0074	0.3536	-0.5158	-1.8136	0.0055	1.7914	0.2346	0.303	1.7992	-0.0552	1.093	16.5436	26.2644	93.6857
26	3.4436	-2.0532	-0.1594	1.4527	-0.3585	0.3561	0.3416	0.7601	-2.1792	1.1175	-0.2201	1.1525	1.625	-1.1095	0.0622	1.0893	-0.1854	0.1886	1.0035	-0.1281	0.9114	22.475	22.2668	76.9164
27	2.7365	-0.1634	-0.2304	1.5656	-3.3752	7.4799	-0.8782	0.0866	1.0697	-0.5734	-1.6609	1.283	-1.0598	-4.6899	-2.0146	1.9074	-0.2681	-0.0314	1.3175	-0.4147	1.4005	16.0457	27.1851	59.413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 120 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 121 through 138 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 31 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 32 through 51 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 52 through 96 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 97 through 120 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 121 through 138 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 6 through 75 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 76 through 96 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 97 through 138 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 6 through 31 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 32 through 96 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 97 through 120 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 121 through 133 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 134 through 138 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 1 through 5 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 6 through 10 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 11 through 15 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 16 through 20 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 21 through 25 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 26 through 30 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 31 through 45 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 46 through 50 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 51 through 55 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 56 through 60 )

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