PDB-5x11: Crystal structure of Bacillus subtilis PadR in complex with opera...

ID or keywords:

Entry

Database: PDB / ID: 5x11

Title

Crystal structure of Bacillus subtilis PadR in complex with operator DNA

Components

(DNA (28-MER)) x 2
Transcriptional regulator

Keywords

TRANSCRIPTION/DNA / Transcription factor / DNA / TRANSCRIPTION-DNA complex

Function / homology

Function and homology information

Transcription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Bacillus subtilis subsp. spizizenii strain W23 (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Park, S.C. / Kwak, Y.M. / Song, W.S. / Hong, M. / Yoon, S.I.

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR
Authors: Park, S.C. / Kwak, Y.M. / Song, W.S. / Hong, M. / Yoon, S.I.

History

Deposition	Jan 24, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2	Dec 27, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	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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Validation report

Summary document	5x11_validation.pdf.gz	520 KB	Display	wwPDB validaton report
Full document	5x11_full_validation.pdf.gz	542 KB	Display
Data in XML	5x11_validation.xml.gz	50.1 KB	Display
Data in CIF	5x11_validation.cif.gz	69.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x1/5x11 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/5x11	HTTPS FTP

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Related structure data

Related structure data	5x12SC 5x13C 5x14C 5y8tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zy8-d 5i92-2 5kr3-d 6ae3-1 2oat-2 5i56-d 4rlj-1 2a2l-d 1n95-d 3wy7-1 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

5x12SC

5x13C

5x14C

5y8tC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

I: DNA (28-MER)

J: DNA (28-MER)

M: DNA (28-MER)

N: DNA (28-MER)

A: Transcriptional regulator

B: Transcriptional regulator

C: Transcriptional regulator

D: Transcriptional regulator

E: Transcriptional regulator

F: Transcriptional regulator

G: Transcriptional regulator

H: Transcriptional regulator

208 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

I: DNA (28-MER)

J: DNA (28-MER)

A: Transcriptional regulator

B: Transcriptional regulator

defined by author&software
60.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

M: DNA (28-MER)

N: DNA (28-MER)

E: Transcriptional regulator

F: Transcriptional regulator

defined by author&software
60.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Transcriptional regulator

D: Transcriptional regulator

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

4

G: Transcriptional regulator

H: Transcriptional regulator

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

Unit cell

Length a, b, c (Å)	341.807, 61.567, 120.553
Angle α, β, γ (deg.)	90.00, 107.94, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
1	2	I
2	2	M
1	3	J
2	3	N

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	2 - 139
2	1	1	5	B	2 - 139
3	1	1	5	C	2 - 139
4	1	1	5	D	2 - 139
5	1	1	5	E	2 - 139
6	1	1	5	F	2 - 139
7	1	1	5	G	2 - 139
8	1	1	5	H	2 - 139
1	2	1	5	A	145 - 176
2	2	1	5	B	145 - 176
3	2	1	5	C	145 - 176
4	2	1	5	D	145 - 176
5	2	1	5	E	145 - 176
6	2	1	5	F	145 - 176
7	2	1	5	G	145 - 176
8	2	1	5	H	145 - 176
1	1	2	5	I	1 - 28
2	1	2	5	M	1 - 28
1	1	3	5	J	1 - 28
2	1	3	5	N	1 - 28

NCS ensembles :

ID
1
2
3

#1: DNA chain	DNA (28-MER) Mass: 8636.616 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain	DNA (28-MER) Mass: 8569.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein	Transcriptional regulator Mass: 21750.912 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. spizizenii strain W23 (bacteria) Strain: W23 / Gene: padR, BSUW23_04210 / Production host: Escherichia coli (E. coli) / References: UniProt: E0TW95
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.9 Å³/Da / Density % sol: 57.51 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.4 M ammonium sulfate, 0.1 M MES, 0.2 M lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00003 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 2.65→30 Å / Num. obs: 69940 / % possible obs: 99.4 % / Redundancy: 3.6 % / R_merge(I) obs: 0.064 / Net I/σ(I): 31.1
Reflection shell	Resolution: 2.65→2.7 Å / R_merge(I) obs: 0.521

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5X12

5x12

Resolution: 2.65→30 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.909 / SU B: 29.664 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.326 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26819	3328	4.8 %	RANDOM
R_work	0.22817	-	-	-
obs	0.23012	66237	99.33 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.09 Å²	0 Å²	-2 Å²
2-	-	5.69 Å²	0 Å²
3-	-	-	-1.83 Å²

Refinement step

Cycle: 1 / Resolution: 2.65→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11121	2284	0	17	13422

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	13931
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.274	2.181	19287
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.621	5	1403
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.58	23.506	445
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.631	15	1998
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.482	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	2161
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9470
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.241	1.5	7050
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.483	2	11197
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.975	3	6881
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.575	4.5	8090
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	668	MEDIUM POSITIONAL	0.27	0.5
1	B	668	MEDIUM POSITIONAL	0.33	0.5
1	C	668	MEDIUM POSITIONAL	0.43	0.5
1	D	668	MEDIUM POSITIONAL	0.34	0.5
1	E	668	MEDIUM POSITIONAL	0.27	0.5
1	F	668	MEDIUM POSITIONAL	0.32	0.5
1	G	668	MEDIUM POSITIONAL	0.25	0.5
1	H	668	MEDIUM POSITIONAL	0.21	0.5
1	A	510	LOOSE POSITIONAL	0.34	5
1	B	510	LOOSE POSITIONAL	0.42	5
1	C	510	LOOSE POSITIONAL	0.52	5
1	D	510	LOOSE POSITIONAL	0.48	5
1	E	510	LOOSE POSITIONAL	0.38	5
1	F	510	LOOSE POSITIONAL	0.43	5
1	G	510	LOOSE POSITIONAL	0.37	5
1	H	510	LOOSE POSITIONAL	0.5	5
1	A	668	MEDIUM THERMAL	0.3	2
1	B	668	MEDIUM THERMAL	0.27	2
1	C	668	MEDIUM THERMAL	0.27	2
1	D	668	MEDIUM THERMAL	0.33	2
1	E	668	MEDIUM THERMAL	0.25	2
1	F	668	MEDIUM THERMAL	0.21	2
1	G	668	MEDIUM THERMAL	0.34	2
1	H	668	MEDIUM THERMAL	0.28	2
1	A	510	LOOSE THERMAL	0.46	10
1	B	510	LOOSE THERMAL	0.41	10
1	C	510	LOOSE THERMAL	0.4	10
1	D	510	LOOSE THERMAL	0.47	10
1	E	510	LOOSE THERMAL	0.37	10
1	F	510	LOOSE THERMAL	0.32	10
1	G	510	LOOSE THERMAL	0.47	10
1	H	510	LOOSE THERMAL	0.37	10
2	I	574	LOOSE POSITIONAL	0.31	5
2	M	574	LOOSE THERMAL	2.76	10
3	J	568	LOOSE POSITIONAL	0.26	5
3	N	568	LOOSE THERMAL	3.28	10

LS refinement shell

Resolution: 2.65→2.718 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.411	224	-
R_work	0.344	4828	-
obs	-	-	99.45 %

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	4.9279	1.0608	-2.2868	3.5962	-1.1145	4.8729	0.0439	0.2178	0.6766	0.1994	0.0085	0.2809	-0.4485	0.0617	-0.0525	0.4986	0.0454	-0.0893	0.1428	0.0129	0.4669	-36.38	15.825	31.044
2	5.1844	-2.6271	1.2427	6.7966	-0.338	1.8305	0.4276	1.7352	-0.705	-0.7168	-0.3296	0.832	0.2715	0.2238	-0.098	0.6263	0.0444	-0.1165	0.8734	-0.2178	0.4502	-30.108	0.884	9.514
3	6.1122	-1.0014	2.1482	3.7016	-0.2264	4.2194	0.1956	0.6036	-1.2292	-0.0947	-0.1707	0.1894	0.5138	0.0794	-0.0248	0.5529	0.0717	-0.0288	0.2146	-0.2392	0.6782	-12.964	-14.305	27.189
4	3.6845	-1.5564	0.6866	4.9703	-0.0632	2.7743	0.1873	1.3015	0.0367	-0.5376	-0.1814	-0.2554	0.1509	0.7508	-0.0059	0.546	0.0306	-0.1048	0.9168	-0.0655	0.3062	-20.41	6.577	10.253
5	7.6989	-2.6679	0.1524	3.0872	1.6321	6.356	0.6295	1.924	-0.3088	-0.0203	-0.4552	0.1469	0.0607	0.5892	-0.1743	0.5885	0.269	-0.1163	0.9946	-0.1605	0.3296	24.166	17.618	11.463
6	2.9606	0.1271	-0.1257	1.9198	-2.7944	8.0083	0.2724	0.0969	0.4103	0.4676	-0.5942	-0.2567	-1.5361	0.911	0.3219	1.1112	-0.1608	-0.0643	0.3216	0.0462	0.53	17.522	31.54	35.679
7	4.7853	2.2441	1.0992	5.7515	-1.343	5.2774	0.2238	-0.4029	-0.0571	0.0186	-0.3761	-0.1269	-0.3996	0.1028	0.1522	0.4994	0.022	-0.0141	0.2292	0.0519	0.2767	8.227	7.606	48.114
8	3.76	0.1006	-0.6014	2.3045	-2.2587	8.0991	0.2948	0.3003	0.327	0.5141	-0.2668	0.1765	-1.2915	-0.29	-0.0279	0.9358	0.1636	0	0.2245	-0.0351	0.4926	7.445	30.377	30.511
9	2.251	-0.7405	-1.7958	5.4221	-1.7103	3.0934	0.2766	0.2724	0.6942	0.0921	-0.7372	-0.4864	-0.4015	0.2889	0.4606	0.3708	0.049	-0.1886	1.3297	0.2527	1.2845	65.783	35.52	31.477
10	4.0467	-0.4222	1.3687	5.5445	0.6646	2.5353	0.3042	0.0839	-0.1	0.2925	-0.2683	-0.2557	0.2142	0.7193	-0.0359	0.4163	0.1543	-0.0907	1.1692	-0.0853	0.4317	67.103	12.334	46.133
11	5.0655	-0.4164	3.5069	4.9882	1.5175	8.0631	0.939	1.0088	-1.5502	-0.5239	-0.4231	0.3347	1.413	1.4705	-0.5159	0.7878	0.5909	-0.3444	1.1002	-0.4761	0.8677	53.672	-0.534	24.602
12	4.6502	0.0859	0.553	5.3681	-0.1111	2.6978	0.194	-0.4415	-0.1961	0.4207	-0.2122	0.3807	0.1542	0.3375	0.0182	0.3925	0.1105	-0.1211	0.991	-0.1092	0.462	56.345	15.315	47.649
13	5.2148	3.1392	0.0237	3.8836	0.5302	3.0246	0.0383	-0.0406	0.0736	0.0978	-0.1528	0.2842	0.0565	-0.3071	0.1146	0.4391	0.0273	-0.0031	0.2536	-0.0889	0.3732	111.424	20.901	45.587
14	6.1737	0.5832	0.7626	1.4603	-2.3834	8.1409	-0.1305	2.003	-0.9379	-0.0991	-0.0516	-0.1663	0.8346	0.0619	0.1821	0.5926	-0.0069	-0.007	0.8836	-0.433	0.6376	110.56	4.865	23.556
15	10.2233	-3.9249	0.3876	1.8194	-0.7179	1.3166	0.5048	3.0719	0.8865	0.1206	-0.3419	-0.2635	-0.4439	-0.8203	-0.163	0.4931	0.1882	0.1143	2.8992	0.3483	0.4786	93.243	24.194	9.587
16	5.1515	0.8555	0.6386	1.3865	-0.5756	6.7946	0.0245	1.5169	-0.9508	-0.1006	0.1968	0.0499	0.7082	-0.7222	-0.2213	0.5717	-0.0991	-0.0171	0.8452	-0.3834	0.6751	100.105	2.716	27.212
17	10.9478	-0.4003	0.2386	0.7297	-0.4235	1.0615	-0.2611	0.5848	-0.4728	0.0357	0.1284	0.0529	0.0387	-0.034	0.1327	0.3378	-0.0031	-0.0552	0.1276	-0.1136	0.3952	-25.005	-0.269	35.125
18	10.6818	-0.3837	-0.9698	0.9069	0.0038	1.0594	-0.2593	0.3597	0.5052	-0.0202	0.1144	-0.0239	0.0812	0.0097	0.1448	0.3469	0.0148	-0.0912	0.1056	-0.0372	0.3393	-25.548	0.511	35.212
19	15.2508	3.558	3.1031	2.4875	0.5127	0.8663	0.305	1.354	0.0286	-0.0508	-0.3414	0.0088	0.3355	0.5965	0.0363	0.3697	0.3311	-0.0638	1.5853	-0.0604	0.3277	59.569	18.423	21.791
20	8.8387	2.06	2.1027	2.7522	-0.0571	0.9622	-0.0603	1.1673	0.2866	-0.283	-0.1076	0.0186	0.2909	0.7594	0.1679	0.2906	0.2844	-0.0858	1.6457	0.0131	0.3464	59.812	19.338	21.929

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 86
2	X-RAY DIFFRACTION	2	A	87 - 179
3	X-RAY DIFFRACTION	3	B	-1 - 86
4	X-RAY DIFFRACTION	4	B	87 - 180
5	X-RAY DIFFRACTION	5	C	2 - 86
6	X-RAY DIFFRACTION	6	C	87 - 180
7	X-RAY DIFFRACTION	7	D	2 - 86
8	X-RAY DIFFRACTION	8	D	87 - 180
9	X-RAY DIFFRACTION	9	E	-1 - 86
10	X-RAY DIFFRACTION	10	E	87 - 179
11	X-RAY DIFFRACTION	11	F	0 - 86
12	X-RAY DIFFRACTION	12	F	87 - 180
13	X-RAY DIFFRACTION	13	G	0 - 86
14	X-RAY DIFFRACTION	14	G	87 - 177
15	X-RAY DIFFRACTION	15	H	2 - 86
16	X-RAY DIFFRACTION	16	H	87 - 180
17	X-RAY DIFFRACTION	17	I	1 - 28
18	X-RAY DIFFRACTION	18	J	1 - 28
19	X-RAY DIFFRACTION	19	M	1 - 28
20	X-RAY DIFFRACTION	20	N	1 - 28

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