PDB-5x5l: Crystal structure of response regulator AdeR DNA binding domain i...

ID or keywords:

Entry

Database: PDB / ID: 5x5l

Title

Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region

Components

AdeR
DNA (5'-D(P*TP*AP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*TP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*A)-3')
DNA (5'-D(P*TP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*AP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*TP*A)-3')

Keywords

DNA BINDING PROTEIN/DNA / bacterial signaling transduction / two-component regulatory system / response regulator / AdeR / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Wen, Y.

Funding support

China, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region.
Authors: Wen, Y. / Ouyang, Z. / Yu, Y. / Zhou, X. / Pei, Y. / Devreese, B. / Higgins, P.G. / Zheng, F.

History

Deposition	Feb 16, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 30, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	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 / refine_hist / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	5x5jSC 5xjpC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ezr-d 1774 5zzb-d 5fet-d 1p16-d 5dyk-d 1775 6pbc-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: AdeR

B: AdeR

E: AdeR

H: AdeR

M: AdeR

N: AdeR

C: DNA (5'-D(P*TP*AP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*TP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*A)-3')

D: DNA (5'-D(P*TP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*AP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*TP*A)-3')

F: DNA (5'-D(P*TP*AP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*TP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*A)-3')

G: DNA (5'-D(P*TP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*AP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*TP*A)-3')

107 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	55.510, 71.380, 78.360
Angle α, β, γ (deg.)	101.96, 104.53, 101.86
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	PRO	PRO	A	A	141 - 240	3 - 102
2	1	LYS	LYS	PRO	PRO	B	B	141 - 240	3 - 102
1	2	LYS	LYS	ASN	ASN	A	A	141 - 239	3 - 101
2	2	LYS	LYS	ASN	ASN	E	C	141 - 239	3 - 101
1	3	LYS	LYS	PRO	PRO	A	A	141 - 240	3 - 102
2	3	LYS	LYS	PRO	PRO	H	D	141 - 240	3 - 102
1	4	LYS	LYS	ASN	ASN	A	A	141 - 239	3 - 101
2	4	LYS	LYS	ASN	ASN	M	E	141 - 239	3 - 101
1	5	LYS	LYS	ASP	ASP	A	A	141 - 238	3 - 100
2	5	LYS	LYS	ASP	ASP	N	F	141 - 238	3 - 100
1	6	ASN	ASN	ASN	ASN	B	B	140 - 239	2 - 101
2	6	ASN	ASN	ASN	ASN	E	C	140 - 239	2 - 101
1	7	ASN	ASN	PRO	PRO	B	B	140 - 240	2 - 102
2	7	ASN	ASN	PRO	PRO	H	D	140 - 240	2 - 102
1	8	ASN	ASN	ASN	ASN	E	C	140 - 239	2 - 101
2	8	ASN	ASN	ASN	ASN	H	D	140 - 239	2 - 101
1	9	ASN	ASN	ASN	ASN	E	C	140 - 239	2 - 101
2	9	ASN	ASN	ASN	ASN	M	E	140 - 239	2 - 101
1	10	ASN	ASN	ASP	ASP	E	C	140 - 238	2 - 100
2	10	ASN	ASN	ASP	ASP	N	F	140 - 238	2 - 100
1	11	ASN	ASN	ASN	ASN	H	D	140 - 239	2 - 101
2	11	ASN	ASN	ASN	ASN	M	E	140 - 239	2 - 101
1	12	ASN	ASN	ASP	ASP	H	D	140 - 238	2 - 100
2	12	ASN	ASN	ASP	ASP	N	F	140 - 238	2 - 100
1	13	ASN	ASN	ASP	ASP	M	E	140 - 238	2 - 100
2	13	ASN	ASN	ASP	ASP	N	F	140 - 238	2 - 100
1	14	DT	DT	DA	DA	C	G	1 - 24	1 - 24
2	14	DT	DT	DA	DA	F	I	1 - 24	1 - 24
1	15	DT	DT	DA	DA	D	H	0 - 24	1 - 25
2	15	DT	DT	DA	DA	G	J	0 - 24	1 - 25

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	AdeR Mass: 12709.622 Da / Num. of mol.: 6 / Fragment: DNA-binding (UNP 139-247) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: adeR / Production host: Escherichia coli (E. coli) / References: UniProt: E1A0Z5
#2: DNA chain	DNA (5'-D(PTPAPAPAPGPTPGPTPGPGPAPGPTPAPAPGPTPGPTPGPGPAPGPA)-3') Mass: 7891.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain	DNA (5'-D(PTPCPTPCPCPAPCPAPCPTPTPAPCPTPCPCPAPCPAPCPTPTPTPA)-3') Mass: 7463.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.65 Å³/Da / Density % sol: 53.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium citrate dibasic, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Nov 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.75→43.821 Å / Num. obs: 27914 / % possible obs: 97.95 % / Redundancy: 3.6 % / Net I/σ(I): 9.97

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0171	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5X5J

5x5j

Resolution: 2.75→43.821 Å / Cor.coef. F_o:F_c: 0.832 / Cor.coef. F_o:F_c free: 0.811 / SU B: 53.203 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R: 1.684 / ESU R Free: 0.495 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2958	2000	8.5 %	RANDOM
R_work	0.27781	-	-	-
obs	0.27933	21666	83.03 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 58.275 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.18 Å²	5.79 Å²	-0.71 Å²
2-	-	3.69 Å²	-0.27 Å²
3-	-	-	-2.68 Å²

Refinement step

Cycle: 1 / Resolution: 2.75→43.821 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4653	2007	0	7	6667

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.017	6964
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	5642
X-RAY DIFFRACTION	r_angle_refined_deg	1.548	1.687	9774
X-RAY DIFFRACTION	r_angle_other_deg	1.282	3	13151
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.825	5	545
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.831	24.348	230
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.727	15	951
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.818	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	1027
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6144
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1366
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	5208	0.13
1	2	B	5208	0.13
2	1	A	5580	0.13
2	2	E	5580	0.13
3	1	A	5602	0.12
3	2	H	5602	0.12
4	1	A	5268	0.15
4	2	M	5268	0.15
5	1	A	4902	0.15
5	2	N	4902	0.15
6	1	B	5156	0.13
6	2	E	5156	0.13
7	1	B	5240	0.11
7	2	H	5240	0.11
8	1	E	5578	0.11
8	2	H	5578	0.11
9	1	E	5430	0.13
9	2	M	5430	0.13
10	1	E	5004	0.14
10	2	N	5004	0.14
11	1	H	5388	0.12
11	2	M	5388	0.12
12	1	H	5080	0.13
12	2	N	5080	0.13
13	1	M	5074	0.15
13	2	N	5074	0.15
14	1	C	4574	0.06
14	2	F	4574	0.06
15	1	D	4176	0.04
15	2	G	4176	0.04

LS refinement shell

Resolution: 2.75→2.822 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.58	18	-
R_work	0.468	195	-
obs	-	-	10.09 %

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	4.2173	-0.0214	-0.4439	2.9758	0.4377	2.3573	-0.0058	0.0182	0.3012	-0.0841	-0.006	0.3695	-0.2329	-0.3352	0.0119	0.3997	-0.1301	-0.0497	0.1362	-0.0436	0.3174	23.237	31.669	30.776
2	3.743	-0.53	0.8293	2.9893	0.3746	3.0587	-0.0788	0.2212	0.0027	-0.0634	0.0562	0.2865	-0.2675	-0.5261	0.0226	0.4613	-0.1244	0.004	0.2155	-0.0411	0.2739	10.171	7.328	1.155
3	3.313	-1.1409	0.0568	5.1212	-0.4693	2.4831	-0.0814	-0.1532	-0.1109	0.0631	0.0953	0.2846	-0.0664	-0.413	-0.0139	0.3771	-0.1748	-0.0115	0.1775	-0.0301	0.3051	11.804	2.749	27.111
4	5.4076	1.2726	-0.813	3.2078	0.3594	5.1579	-0.2282	-0.0472	0.3532	-0.2356	0.2195	0.1045	-0.4199	-0.2411	0.0086	0.6055	-0.1664	-0.0441	0.0981	-0.0279	0.2667	28.583	31.823	4.536
5	4.1815	-0.7774	1.1817	2.9619	-0.0549	2.6484	-0.1335	-0.4722	-0.1967	0.1733	0.0916	-0.1499	0.2172	0.1797	0.0419	0.4797	-0.1171	-0.0201	0.1727	-0.0204	0.3413	1.094	29.937	51.965
6	6.0971	-1.6721	1.5217	3.0769	-0.0563	1.9786	-0.1425	-0.0409	0.3193	0.0611	-0.0259	0.3835	-0.3456	-0.2512	0.1684	0.5176	-0.1199	-0.0063	0.1054	-0.0446	0.2677	36.407	55.17	44.694
7	2.1339	1.9558	-0.0727	4.7749	0.3322	1.0727	-0.2737	0.1286	-0.2785	-0.6147	0.1274	-0.5754	-0.0003	0.0589	0.1463	0.6114	-0.265	0.0517	0.1292	0.0119	0.3854	33.711	14.568	-5.238
8	1.7568	1.1529	-0.092	3.8723	-0.0122	1.8481	-0.2748	0.0982	-0.0366	-0.5384	0.1874	-0.276	0.0074	0.1358	0.0873	0.5158	-0.244	0.0289	0.1311	-0.0369	0.3356	31.84	13.701	-5.08
9	2.6062	3.1396	0.7051	5.638	0.8198	0.5801	0.0862	-0.2156	-0.5682	-0.054	-0.2287	-0.7278	0.0709	-0.0937	0.1425	0.4968	-0.2871	0.0269	0.1796	0.0281	0.5151	28.998	6.379	36.842
10	2.0552	1.9061	-0.7335	2.7559	-1.5406	1.7171	0.3787	-0.2606	-0.1688	0.3285	-0.4065	-0.297	-0.0782	0.1523	0.0278	0.6212	-0.3276	0.0096	0.2103	0.0121	0.6531	28.78	8.568	36.777

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	141 - 240
2	X-RAY DIFFRACTION	2	B	140 - 243
3	X-RAY DIFFRACTION	3	E	140 - 239
4	X-RAY DIFFRACTION	4	H	140 - 240
5	X-RAY DIFFRACTION	5	M	140 - 239
6	X-RAY DIFFRACTION	6	N	140 - 238
7	X-RAY DIFFRACTION	7	C	1 - 24
8	X-RAY DIFFRACTION	8	D	0 - 24
9	X-RAY DIFFRACTION	9	F	1 - 24
10	X-RAY DIFFRACTION	10	G	0 - 24

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