PDB-4ua2: Crystal structure of dual function transcriptional regulator MerR...

ID or keywords:

Entry

Database: PDB / ID: 4ua2

Title

Crystal structure of dual function transcriptional regulator MerR from Bacillus megaterium MB1

Components

Regulatory protein

Keywords

DNA BINDING PROTEIN / Metalloregulatory protein

Function / homology

Function and homology information

mercury ion binding / response to mercury ion / DNA-binding transcription factor activity / DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Bacillus megaterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.61 Å

Authors

Lin, L.Y. / Chang, C.C. / Zou, X.W. / Huang, C.C. / Chan, N.L.

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Structural basis of the mercury(II)-mediated conformational switching of the dual-function transcriptional regulator MerR
Authors: Chang, C.C. / Lin, L.Y. / Zou, X.W. / Huang, C.C. / Chan, N.L.

History

Deposition	Aug 7, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2015	Group: Database references
Revision 1.2	Jan 29, 2020	Group: Data collection / Database references / Derived calculations Category: citation / diffrn_source / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ua2.cif.gz	377.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ua2.ent.gz	312.6 KB	Display	PDB format
PDBx/mmJSON format	4ua2.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/ua/4ua2 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/4ua2	HTTPS FTP

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Related structure data

Related structure data	4ua1C C: citing same article (ref.)
Similar structure data	4gcy-d 3mix-d 5qls-d 5ql4-d 5ql3-d 2h5y-5 2w73-1 6ceq-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) 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

4ua1C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Regulatory protein

G: Regulatory protein

E: Regulatory protein

C: Regulatory protein

F: Regulatory protein

B: Regulatory protein

D: Regulatory protein

H: Regulatory protein

131 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Regulatory protein

B: Regulatory protein

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

2

G: Regulatory protein

H: Regulatory protein

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

3

E: Regulatory protein

F: Regulatory protein

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

4

C: Regulatory protein

D: Regulatory protein

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

Unit cell

Length a, b, c (Å)	80.542, 94.806, 87.060
Angle α, β, γ (deg.)	90.00, 101.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Regulatory protein Mass: 16327.011 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: MB1 / Gene: merR / Plasmid: pET-21b / Details (production host): 21b-MerR / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: Q799U3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, ammonium phosphate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL12B2 / Wavelength: 1.0, 0.97914, 0.95370

Detector

Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 26, 2010

Radiation

Monochromator: LN2-Cool, Fixed-Exit Double Crystal Monochromator (Crystal type Si(111))
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.97914	1
3	0.9537	1

Reflection

Resolution: 2.61→30 Å / Num. obs: 38508 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 24.3

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement

Refinement

Resolution: 2.61→28.411 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2574	1926	5.01 %
R_work	0.2251	-	-
obs	0.2267	38480	99.06 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.61→28.411 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7166	0	0	97	7263

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7238
X-RAY DIFFRACTION	f_angle_d	0.67	9710
X-RAY DIFFRACTION	f_dihedral_angle_d	11.659	2814
X-RAY DIFFRACTION	f_chiral_restr	0.024	1126
X-RAY DIFFRACTION	f_plane_restr	0.003	1240

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 (%)
2.6155-2.6809	0.3024	130	0.283	2575	X-RAY DIFFRACTION	97
2.6809-2.7533	0.3232	148	0.2865	2581	X-RAY DIFFRACTION	100
2.7533-2.8343	0.3031	124	0.2761	2635	X-RAY DIFFRACTION	100
2.8343-2.9257	0.2909	124	0.2646	2636	X-RAY DIFFRACTION	100
2.9257-3.0301	0.2989	145	0.2616	2613	X-RAY DIFFRACTION	100
3.0301-3.1513	0.3015	133	0.265	2624	X-RAY DIFFRACTION	100
3.1513-3.2945	0.3072	144	0.2493	2608	X-RAY DIFFRACTION	100
3.2945-3.4679	0.2804	115	0.2264	2657	X-RAY DIFFRACTION	99
3.4679-3.6848	0.2795	159	0.2117	2588	X-RAY DIFFRACTION	100
3.6848-3.9686	0.2402	155	0.2038	2619	X-RAY DIFFRACTION	100
3.9686-4.3666	0.2145	121	0.1928	2644	X-RAY DIFFRACTION	100
4.3666-4.9955	0.1993	136	0.1865	2628	X-RAY DIFFRACTION	99
4.9955-6.2826	0.2839	147	0.2421	2636	X-RAY DIFFRACTION	99
6.2826-28.4122	0.2283	145	0.2169	2510	X-RAY DIFFRACTION	93

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	3.5201	-0.1366	-1.8507	4.4388	-1.5133	6.8205	0.1914	-0.6999	-0.3994	1.1626	-0.2557	0.1097	0.7016	-0.2991	0.0792	0.7843	-0.1835	0.004	0.5824	0.0775	0.418	7.663	76.2557	49.5994
2	2.668	1.6665	1.9052	3.8635	2.7217	4.6706	0.2847	-0.0634	-0.3321	0.0407	-0.2486	-0.3205	0.3825	0.0317	-0.0384	0.3645	0.0316	-0.0513	0.2751	0.0562	0.3709	16.2393	70.155	24.6617
3	6.905	-1.0946	3.539	5.9162	-3.5754	3.395	-0.6192	-1.356	-0.7611	0.1429	0.7374	0.3105	0.1701	-2.829	0.2976	0.7675	-0.0024	0.2454	1.0327	0.0933	0.7558	-12.5423	57.7214	31.0109
4	7.1988	-1.2649	-1.3498	3.0519	-4.6251	8.7265	-0.2808	-0.0576	-0.7305	0.2265	-0.1235	-0.4508	1.0789	-0.5188	0.3017	0.6054	-0.1115	0.0422	0.5834	-0.0888	0.4461	-5.4777	59.0594	26.9431
5	3.4441	-0.5291	-2.9439	4.3513	1.7523	6.8961	0.3263	0.8568	-1.1594	-0.5625	-1.0915	1.2824	0.4916	-1.5058	0.6834	0.4773	-0.0091	-0.1489	0.5631	-0.1858	0.6351	-5.7877	59.7502	13.8321
6	0.9723	-0.5593	-0.6469	3.9721	4.6283	5.2925	0.2479	0.1168	0.1008	-0.5514	-0.2748	0.162	-0.4714	-0.4531	-0.0598	0.4522	0.088	-0.0294	0.3928	-0.0326	0.3552	-0.5942	80.948	17.0541
7	4.1976	-4.3314	1.8187	7.3981	-6.3668	8.4079	-0.0479	-0.4028	-0.1717	0.0101	-0.1245	0.7404	-0.1061	-0.26	0.2033	0.3695	-0.067	0.063	0.3691	-0.1823	0.3768	4.1474	90.0645	39.7998
8	3.054	-0.2019	-3.3901	9.5642	-1.9975	5.4917	0.6716	1.1815	-0.5381	-1.1287	-0.2755	2.0394	0.2435	-0.5758	-0.3121	1.0429	0.0889	-0.3759	0.4748	0.0049	1.0528	-10.5454	87.1394	-11.8565
9	5.9108	0.6182	2.6727	8.2562	-0.7743	5.0683	0.2984	0.7141	0.1128	-1.1906	-0.0153	0.5718	0.1603	0.4878	-0.1941	0.6836	0.051	-0.1535	0.484	0.0704	0.4258	2.1518	82.2965	-7.555
10	2.1529	-1.183	-1.9221	5.079	3.8031	6.6934	-0.1497	0.1657	-0.0075	-0.173	-0.2299	0.0376	-0.0552	0.2851	0.3759	0.4377	0.0784	-0.0047	0.3807	0.0387	0.341	13.8921	91.1826	7.5599
11	4.599	5.571	2.3939	6.9915	2.358	4.1689	-0.2974	0.3579	0.6278	-0.9083	-0.0637	0.6626	-0.7411	-0.4293	0.2511	0.4171	0.0783	0.0292	0.3636	0.0271	0.478	-2.652	101.0577	23.5502
12	3.6511	4.4506	-0.8011	5.1244	-1.6695	5.8285	-0.8277	1.1265	0.2	-0.8425	0.6368	-0.3093	-0.2491	2.2375	0.2021	0.6569	-0.2602	0.0344	1.3347	0.232	0.6725	37.6891	81.4548	0.2325
13	1.2959	-2.3184	-0.6943	7.7305	0.9671	2.1016	0.1645	0.0992	0.1364	0.0008	-0.4482	-0.3489	-0.1152	0.3429	0.2289	0.2668	-0.0625	-0.0257	0.4381	0.0485	0.41	24.3992	91.6598	19.634
14	0.6637	-0.6949	0.1254	0.7412	-0.2156	0.0628	0.6734	0.7448	0.6551	0.0033	-0.1766	0.2214	0.1236	0.4114	-0.2123	0.6942	-0.358	0.2206	1.5761	0.1996	0.8731	25.927	110.1541	-3.9923
15	6.2152	-4.2791	-2.8974	8.0814	1.8801	1.3468	-0.4399	0.1578	1.7012	-0.3271	0.2226	-0.9148	-1.8478	2.1931	0.153	0.5872	-0.2405	-0.131	1.0709	0.1502	0.5822	18.4234	116.3184	-2.1994
16	3.5971	2.4915	1.5742	5.877	1.1968	4.5983	0.1619	0.1675	0.2414	0.196	-0.3975	0.2024	0.0716	0.4636	0.2173	0.5201	0.0073	-0.0416	0.5057	0.1537	0.3506	12.2168	108.7967	7.3046
17	3.2331	-3.7406	-2.7525	4.43	5.5866	7.2086	-0.256	0.1613	0.0123	0.2344	0.1482	0.0349	0.0485	0.0722	0.0993	0.3755	0.0199	-0.044	0.3095	0.0116	0.3338	6.2202	89.4119	8.6664
18	8.8493	6.2342	4.743	8.4427	0.7491	8.0826	-1.0432	1.138	0.098	-1.46	0.5131	-0.5688	-0.8852	1.0494	0.5237	0.6809	0.0409	0.0772	0.7053	0.0468	0.4642	23.4911	74.6895	-2.8468
19	7.8926	-0.4707	3.4528	3.2816	1.5923	7.0745	0.233	0.0956	-0.1089	0.1557	-0.0361	-0.5158	0.7921	0.886	-0.1786	0.5713	0.1664	-0.0617	0.4963	0.1323	0.4908	33.3172	59.6917	30.2217
20	1.0718	1.1159	0.0563	3.6506	0.6306	1.0984	0.1667	-0.1541	-0.1153	0.2352	-0.1297	0.0987	0.0501	0.0707	-0.0347	0.3805	-0.0296	-0.0698	0.3644	0.0462	0.3227	17.1067	81.528	32.152
21	3.3438	-0.1949	-1.6926	3.995	-0.2656	4.8001	0.2927	0.3478	-1.8439	-0.0917	-0.7721	0.6912	0.8992	-0.6126	-0.2928	0.5356	0.2126	-0.2886	1.1118	0.4495	1.5934	47.5868	82.7818	37.3062
22	3.7693	-0.4004	3.8265	3.5674	-0.4788	4.263	0.2154	-0.5221	-0.2732	0.2336	-0.3672	-0.9879	-0.157	1.0005	0.1678	0.3811	-0.07	-0.0746	1.0187	0.1757	0.7907	42.3817	90.8928	32.0793
23	7.529	-5.8714	-5.7952	8.1906	3.5337	7.8789	0.3894	-0.2581	1.1293	0.3394	-0.1012	-1.2657	-0.8851	0.7194	-0.3475	0.4529	-0.153	-0.0826	0.5446	0.0951	0.5821	35.1456	100.9605	29.5452
24	1.0389	-1.1327	-0.3323	5.7943	7.2566	8.2282	-0.066	0.2576	0.0841	-0.1729	0.0677	-0.8327	-0.2099	0.4864	0.07	0.3872	-0.0154	0.0204	0.4477	0.0885	0.4369	25.7469	88.4468	13.7999
25	4.0813	-1.7659	-0.1544	7.1645	-1.866	2.6397	-0.0681	0.0555	-0.3798	0.1075	0.1173	-0.7125	0.8329	0.9227	-0.1149	0.4273	0.1	0.0919	0.4613	-0.0451	0.5362	28.5703	63.9854	14.3029
26	8.5761	1.3863	3.5238	5.6669	-0.1823	5.7127	0.2801	0.2681	0.1842	-0.0999	-0.1165	1.0363	-0.044	-0.739	-0.2197	0.2917	0.0363	0.0243	0.5136	0.0294	0.5669	-15.7008	92.9495	23.5916
27	5.0801	-5.2577	-3.3394	9.347	5.9293	5.4775	0.1082	-0.2069	-0.2517	0.4077	0.1189	0.0619	0.4019	-0.0561	-0.268	0.4356	-0.0217	-0.0235	0.3172	0.0127	0.2922	1.3405	77.655	24.1419
28	3.6643	-1.993	1.9862	6.893	-5.6854	9.1056	0.2104	0.0505	-0.4172	-0.7895	-0.218	0.9347	0.4688	-0.2134	0.0971	0.58	-0.0161	-0.119	0.3813	-0.111	0.4759	3.1581	70.4084	0.0537

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 130 )
3	X-RAY DIFFRACTION	3	chain 'G' and (resid 8 through 25 )
4	X-RAY DIFFRACTION	4	chain 'G' and (resid 26 through 57 )
5	X-RAY DIFFRACTION	5	chain 'G' and (resid 58 through 81 )
6	X-RAY DIFFRACTION	6	chain 'G' and (resid 82 through 112 )
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 113 through 130 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 6 through 42 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 43 through 81 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 82 through 113 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 114 through 130 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 16 through 81 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 82 through 130 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 5 through 15 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 16 through 45 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 46 through 81 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 82 through 112 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 113 through 130 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 4 through 81 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 82 through 130 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 4 through 15 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 16 through 57 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 58 through 81 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 82 through 112 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 113 through 131 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 16 through 81 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 82 through 112 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 113 through 131 )

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi