PDB-5x80: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTE...

ID or keywords:

Entry

Database: PDB / ID: 5x80

Title

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTEIN RV2887 COMPLEX WITH SALICYLIC ACID

Components

Uncharacterized HTH-type transcriptional regulator Rv2887

Keywords

TRANSCRIPTION / WHTH MOTIF / HTH-TYPE TRANSCRIPTIONAL REGULATOR / DNA BINDING / P-AMINOSALICYLIC ACID 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 H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 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	Feb 28, 2017	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Aug 9, 2017	ID: 5HSN
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	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	5x80.cif.gz	213 KB	Display	PDBx/mmCIF format
PDB format	pdb5x80.ent.gz	170.7 KB	Display	PDB format
PDBx/mmJSON format	5x80.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5x80_validation.pdf.gz	489.9 KB	Display	wwPDB validaton report
Full document	5x80_full_validation.pdf.gz	495.7 KB	Display
Data in XML	5x80_validation.xml.gz	21.7 KB	Display
Data in CIF	5x80_validation.cif.gz	30.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/5x80 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/5x80	HTTPS FTP

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Related structure data

Related structure data	5hsmC 5hsoC 5x7zSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5mtx-d 3zsi-d 4egq-2 3qbt-1 3obg-d 3oef-d 4z9l-d 6bio-d 5tco-d 4nkg-2 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
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #17 - May 2001 Cyclooxygenase similarity (1)

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

hetero molecules

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

1

A: Uncharacterized HTH-type transcriptional regulator Rv2887

B: Uncharacterized HTH-type transcriptional regulator Rv2887

hetero molecules

defined by author&software
Evidence: gel filtration, The gel filtration data comfirmed that Rv2887 exists as a dimer in solution.
34.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Uncharacterized HTH-type transcriptional regulator Rv2887

D: Uncharacterized HTH-type transcriptional regulator Rv2887

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.970, 44.150, 122.160
Angle α, β, γ (deg.)	90.00, 90.42, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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 H37Rv (bacteria) Strain: H37Rv / Gene: Rv2887, MTCY274.18 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WME9
#2: Chemical	ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₆O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.3 Å³/Da / Density % sol: 46.46 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M CITRIC ACID, PH 3.5, 2.0M AMMONIUM SULFATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 21, 2012 / Details: MIRRORS
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.4→57.97 Å / Num. obs: 21945 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / B_iso Wilson estimate: 42 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.061 / R_pim(I) all: 0.037 / R_sym value: 0.061 / Net I/av σ(I): 7.7 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.207 / Mean I/σ(I) obs: 5 / Num. unique obs: 2932 / CC_1/2: 0.966 / R_pim(I) all: 0.124 / R_sym value: 0.207 / % possible all: 82.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5X7Z

5x7z

Resolution: 2.4→57.968 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.45

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2589	2005	9.17 %	RANDOM
R_work	0.231	-	-	-
obs	0.2336	21860	88.69 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→57.968 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3851	0	50	144	4045

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3948
X-RAY DIFFRACTION	f_angle_d	1.257	5340
X-RAY DIFFRACTION	f_dihedral_angle_d	12.592	2486
X-RAY DIFFRACTION	f_chiral_restr	0.059	636
X-RAY DIFFRACTION	f_plane_restr	0.007	691

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 (%)
2.4002-2.4602	0.3364	122	0.2572	1208	X-RAY DIFFRACTION	76
2.4602-2.5267	0.2708	134	0.2481	1400	X-RAY DIFFRACTION	89
2.5267-2.6011	0.2859	148	0.2467	1417	X-RAY DIFFRACTION	89
2.6011-2.685	0.2993	130	0.2436	1387	X-RAY DIFFRACTION	89
2.685-2.781	0.3036	147	0.2727	1459	X-RAY DIFFRACTION	90
2.781-2.8923	0.3437	145	0.273	1403	X-RAY DIFFRACTION	89
2.8923-3.024	0.3194	145	0.2669	1413	X-RAY DIFFRACTION	90
3.024-3.1834	0.3005	139	0.2725	1438	X-RAY DIFFRACTION	91
3.1834-3.3828	0.3156	148	0.2575	1452	X-RAY DIFFRACTION	91
3.3828-3.644	0.2144	147	0.2219	1432	X-RAY DIFFRACTION	89
3.644-4.0106	0.2629	139	0.2255	1389	X-RAY DIFFRACTION	88
4.0106-4.5907	0.2063	149	0.1799	1463	X-RAY DIFFRACTION	91
4.5907-5.783	0.2293	152	0.2106	1486	X-RAY DIFFRACTION	92
5.783-57.9853	0.2111	160	0.2121	1508	X-RAY DIFFRACTION	90

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	7.6272	2.6181	-0.6358	2.6102	-0.3788	5.0828	0.15	-0.9853	0.2501	0.6055	0.0981	1.6278	-0.0971	0.1339	-0.8683	0.382	-0.0384	-0.043	0.5968	0.1026	0.411	34.7332	22.9213	90.9436
2	5.2051	2.1346	-2.7761	4.9974	-2.8514	3.5921	0.3084	0.1341	0.2348	0.282	-0.0326	0.3206	-0.9502	-0.727	-0.2575	0.2352	0.0358	-0.0201	0.2083	-0.0241	0.2952	45.2448	23.1066	74.159
3	6.2291	0.2612	-2.3464	3.907	1.697	4.0898	0.0674	0.2984	-0.4658	-0.1442	-0.2332	0.3255	-0.0852	-0.627	0.1342	0.3124	0.0292	-0.0452	0.2893	-0.043	0.2424	45.6679	12.5466	59.9045
4	1.3166	0.603	-0.4535	5.2797	4.1727	6.8635	0.1429	0.1593	-0.0934	-0.5532	-0.1167	-0.2201	-0.4787	-0.2846	-0.0438	0.1949	0.0556	0.0301	0.2732	0.0521	0.2746	54.5361	13.4665	60.1077
5	8.0697	6.6325	3.9892	5.4166	3.3769	2.6047	0.1206	-0.092	-1.0437	0.4885	0.3519	-1.1823	0.1354	0.3811	-0.349	0.2253	-0.0073	0.0105	0.3709	0.0362	0.3383	55.8331	15.4518	85.3484
6	4.8915	2.6768	-4.5905	4.1222	-2.8856	5.1506	-0.2818	0.3203	-1.5649	-0.2838	-0.2108	-0.4955	0.2816	0.0169	0.3015	0.3174	-0.0032	-0.0574	0.2689	-0.0364	0.3245	43.4595	8.4251	77.9263
7	3.7631	0.1346	-1.0256	4.2292	-1.1415	5.0876	0.1574	0.8659	0.1984	-0.2618	-0.0492	0.5506	-0.3193	-0.6715	-0.021	0.2514	0.0653	0.0057	0.4753	-0.0282	0.3969	22.0044	19.575	78.4619
8	2.1325	-1.3953	1.0963	4.6078	-2.0488	3.1585	-0.3326	-0.9305	-0.8791	0.2302	0.4637	0.3964	0.06	-0.4854	0.1109	0.3048	-0.0319	0.0721	0.3039	-0.0059	0.2601	31.0012	9.9027	90.5455
9	2.731	-1.6735	1.3335	3.5182	-4.7712	7.7968	-0.415	-0.7811	0.2919	1.3739	0.4573	-0.3331	-0.8557	-0.3958	-0.0064	0.3943	0.0419	-0.0186	0.3478	-0.014	0.2856	48.6974	16.7535	91.6085
10	1.1467	-1.4387	-1.314	4.8346	2.766	6.2677	0.3836	-0.3065	0.2071	0.047	0.1004	-0.5012	-0.6508	0.6973	-0.4629	0.2901	-0.0799	0.0213	0.2956	-0.0215	0.2964	10.0211	0.7647	106.649
11	4.4632	1.1458	-2.7323	5.4113	-0.3703	4.6251	0.0309	-0.509	-0.1999	0.1726	-0.2912	-0.2303	0.1098	0.6498	0.2746	0.4018	0.0064	-0.0544	0.4097	0.0632	0.2795	10.3031	-9.9893	122.8568
12	1.8634	-1.2679	0.8916	4.6892	-2.5959	8.1581	0.0798	-0.1579	-0.0575	0.6686	-0.055	0.266	-0.7866	-0.592	0.1067	0.3819	-0.0152	0.072	0.3008	-0.0518	0.2202	-1.3539	-0.7984	115.9555
13	7.5361	-4.5454	1.1572	3.9393	-2.6686	4.1682	-0.5132	-0.0926	-0.9521	0.9713	0.6966	1.148	0.2804	-0.7818	-0.2957	0.342	-0.071	0.0404	0.3758	-0.0388	0.3704	-2.2423	-7.261	98.3999
14	9.183	-3.9966	-4.161	4.6941	1.8329	3.5055	-0.037	-0.7634	-0.4799	0.3119	-0.04	0.406	0.0792	0.1951	0.0033	0.2207	-0.031	-0.0097	0.2413	-0.034	0.2247	12.6161	-13.7212	102.4402
15	2.8686	-0.5728	-1.5438	3.4188	-0.7389	4.6823	0.0891	0.1943	0.4061	0.5773	0.0399	-0.0077	-0.4641	0.2793	-0.0495	0.3817	-0.0761	-0.0683	0.3301	0.0275	0.3886	26.9719	-4.7251	97.8759
16	5.926	0.974	-2.1646	7.0301	-0.4977	8.91	0.5351	-0.7063	0.4574	0.9516	-0.3011	-0.7243	-0.1099	0.4318	-0.0751	0.3576	-0.0896	-0.0002	0.4492	0.0097	0.3566	29.9	-5.5485	106.1108
17	2.7868	-2.5509	-0.6019	6.3422	-5.531	9.1854	0.382	-0.3751	0.8406	1.3691	-0.2031	-0.703	-2.0991	1.4732	0.1435	0.3356	-0.0341	-0.2016	0.4232	0.1101	0.9519	37.8038	-1.8959	96.4306
18	2.7075	0.4528	0.9388	3.7059	0.5995	3.5966	-0.2229	0.1343	-0.1444	-0.1147	-0.1551	-0.1193	0.1223	0.3539	0.0776	0.2038	0.0738	0.0488	0.2526	0.0195	0.2791	21.4872	-12.094	89.7181
19	6.5088	1.7497	0.8816	3.2617	5.1042	9.3179	-0.052	0.5498	0.7339	-1.1015	0.0135	0.2335	-1.3826	-0.8421	-0.2073	0.3806	0.0386	0.0116	0.3676	0.011	0.2531	3.574	-5.2577	90.9743

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 8 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 9 through 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 80 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 81 through 120 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 121 through 137 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 31 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 32 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 137 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 7 through 31 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 32 through 96 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 97 through 120 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 121 through 138 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 6 through 31 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 32 through 51 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 52 through 75 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 76 through 96 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 97 through 120 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 121 through 137 )

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