PDB-5e3j: The response regulator RstA is a potential drug target for Acinet...

ID or keywords:

Entry

Database: PDB / ID: 5e3j

Title

The response regulator RstA is a potential drug target for Acinetobacter baumannii

Components

Response regulator RstA

Keywords

TRANSCRIPTION / response regulator / Acinetobacter baumannii / essential gene / antibiotic target

Function / homology

Function and homology information

phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Russo, T.A. / Manohar, A. / Beanan, J.M. / Olson, R. / MacDonald, U. / Graham, J. / Umland, T.C.

Funding support

United States, 5items

Organization	Grant number	Country
Telemedicine and Advance Technical Research Center	W23RYX1055N607	United States
Interdisciplinary Grant from the University at Buffalo		United States
Veterans Administration		United States
Department of Energy (DOE, United States)	DE-AC02-76SF00515	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM103393	United States

Citation

Journal: Msphere / Year: 2016
Title: The Response Regulator BfmR Is a Potential Drug Target for Acinetobacter baumannii.
Authors: Russo, T.A. / Manohar, A. / Beanan, J.M. / Olson, R. / MacDonald, U. / Graham, J. / Umland, T.C.

History

Deposition	Oct 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 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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PDBx/mmCIF format	5e3j.cif.gz	114.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5e3j_validation.pdf.gz	425.8 KB	Display	wwPDB validaton report
Full document	5e3j_full_validation.pdf.gz	426.6 KB	Display
Data in XML	5e3j_validation.xml.gz	12.2 KB	Display
Data in CIF	5e3j_validation.cif.gz	17 KB	Display
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Related structure data

Related structure data	1mvoS S: Starting model for refinement
Similar structure data	5hm6-d 6vbf-d 6br7-d 6is1-2 6is1-3 6n3l-1 3mpo-1 2ooj-d 1ezm-d 6is3-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
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (10) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Response regulator RstA

B: Response regulator RstA

30.1 kDa, 2 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)	52.015, 52.015, 197.861
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Response regulator RstA Mass: 15028.366 Da / Num. of mol.: 2 / Fragment: UNP residues 1-130 Source method: isolated from a genetically manipulated source Details: clinical isolate, Buffalo, NY, USA / Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: ABBFA_002866 / Plasmid: pET15b-TEV Details (production host): modified pET15b plasmid, with a TEV protease cleavage site substituted for the standard thrombin cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0C9D6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Response regulator RstA

Mass: 15028.366 Da / Num. of mol.: 2 / Fragment: UNP residues 1-130
Source method: isolated from a genetically manipulated source
Details: clinical isolate, Buffalo, NY, USA / Source: (gene. exp.)

Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: ABBFA_002866 / Plasmid: pET15b-TEV
Details (production host): modified pET15b plasmid, with a TEV protease cleavage site substituted for the standard thrombin cleavage site
Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0C9D6

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.57 Å³/Da / Density % sol: 52.15 % / Description: rod with hexagonal cross-section
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: crystallization drop contained 2 ul of purified RstA1-130 (in 20 mM Tris-HCl pH 8.0, 200 mM NaCl, and 1 mM DTT) at 11.25 mg/ml plus 2 ul of reservoir solution against 1 ml of reservoir; ...Details: crystallization drop contained 2 ul of purified RstA1-130 (in 20 mM Tris-HCl pH 8.0, 200 mM NaCl, and 1 mM DTT) at 11.25 mg/ml plus 2 ul of reservoir solution against 1 ml of reservoir; crystallization cocktail: 20%(v/v) PEG 400, 20%(v/v/) glycerol, 100 mM Tris-HCl, pH 8.5, and 150 mM NaCl

Crystal

Density Matthews: 2.57 Å³/Da / Density % sol: 52.15 % / Description: rod with hexagonal cross-section

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: crystallization drop contained 2 ul of purified RstA1-130 (in 20 mM Tris-HCl pH 8.0, 200 mM NaCl, and 1 mM DTT) at 11.25 mg/ml plus 2 ul of reservoir solution against 1 ml of reservoir; ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97946 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 12, 2009

Radiation

Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 17580 / % possible obs: 99.3 % / Redundancy: 10.8 % / B_iso Wilson estimate: 24.1 Å² / R_merge(I) obs: 0.086 / Χ²: 0.98 / Net I/σ(I): 20.5 / Num. measured all: 189638

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.1-2.18	6.5	0.401	4.4	1668	1.063	94.3
2.18-2.26	9.3	0.346		1774	1.028	99.6
2.26-2.37	10.7	0.295		1763	1.06	99.9
2.37-2.49	11.3	0.244		1749	1.045	100
2.49-2.65	11.6	0.203		1748	1.042	100
2.65-2.85	11.6	0.156		1756	1.021	100
2.85-3.14	11.7	0.1		1771	0.993	100
3.14-3.59	11.7	0.066		1772	0.962	100
3.59-4.52	11.7	0.048		1771	0.794	100
4.52-50	11.5	0.036		1808	0.861	99.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4 Å	29.73 Å
Translation	4 Å	29.73 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1682	refinement
Blu-Ice		data collection
SCALEPACK		data scaling
MOLREP	6	phasing
PDB_EXTRACT	3.15	data extraction
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1MVO

1mvo

Resolution: 2.1→29.73 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1947	1229	7.02 %	Random Selection
R_work	0.1633	-	-	-
obs	0.1656	17510	99.38 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→29.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1908	0	0	181	2089

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1954
X-RAY DIFFRACTION	f_angle_d	0.832	2649
X-RAY DIFFRACTION	f_dihedral_angle_d	13.39	789
X-RAY DIFFRACTION	f_chiral_restr	0.029	317
X-RAY DIFFRACTION	f_plane_restr	0.005	347

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 (%)
2.1-2.184	0.2551	132	0.2139	1737	X-RAY DIFFRACTION	95
2.184-2.2834	0.2072	137	0.1835	1782	X-RAY DIFFRACTION	100
2.2834-2.4037	0.1868	141	0.1608	1826	X-RAY DIFFRACTION	100
2.4037-2.5542	0.2389	134	0.1675	1814	X-RAY DIFFRACTION	100
2.5542-2.7513	0.226	139	0.177	1828	X-RAY DIFFRACTION	100
2.7513-3.028	0.1915	136	0.1698	1816	X-RAY DIFFRACTION	100
3.028-3.4655	0.2236	140	0.1668	1831	X-RAY DIFFRACTION	100
3.4655-4.364	0.1528	134	0.1444	1814	X-RAY DIFFRACTION	100
4.364-29.7328	0.1754	136	0.1525	1833	X-RAY DIFFRACTION	100

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	0.2988	-0.0897	-0.0052	0.1539	0.0032	0.2204	0.1794	0.1904	0.1148	0.146	-0.0701	-0.1765	-0.0887	-0.0777	-0.0115	0.3227	0.0658	-0.0231	0.1548	0.0115	0.181	52.7113	-14.6348	1.1891
2	0.0597	0.0658	0.0611	0.0655	-0.0166	0.101	0.0323	0.0285	0.0484	0.1045	0.0331	-0.0996	0.1855	0.2499	0.1757	0.3712	0.1199	-0.0716	0.2107	-0.0058	0.2303	60.2772	-12.4186	6.0501
3	0.8506	-0.0825	0.1418	0.1071	0.0357	0.0735	0.0727	0.6169	-0.4498	0.5012	0.1562	-0.1499	0.1855	-0.0496	0.1051	0.4578	0.1395	-0.0422	0.065	0.0796	0.2089	54.4824	-16.9829	0.4104
4	0.2331	0.1974	0.0163	0.3381	-0.0566	0.4559	0.0928	0.0573	-0.1719	0.2202	-0.1495	0.1155	0.2038	0.0834	-0.0121	0.3015	0.0602	-0.0105	0.1638	-0.018	0.2251	48.8768	-17.6851	-6.1535
5	0.0624	-0.0672	-0.0174	0.079	0.0512	0.0911	0.2679	0.2543	0.2638	0.1713	0.2084	-0.3498	-0.0469	0.1822	0.0606	0.2086	0.0973	0.0061	0.2929	-0.0063	0.2777	57.386	-9.8185	-12.8909
6	0.1887	-0.0123	0.1907	0.0429	0.0942	0.6302	0.1395	0.2417	0.2979	-0.1427	-0.2083	0.1403	0.02	-0.3698	-0.0166	0.2164	0.078	-0.0272	0.2585	-0.0592	0.2133	45.1881	-12.1304	-14.0463
7	0.1261	-0.0234	0.134	0.2916	-0.138	0.3882	-0.1504	0.137	0.1671	-0.4143	-0.0465	0.0765	-0.3789	-0.0851	-0.0655	0.2644	0.069	-0.0199	0.212	-0.0089	0.1956	50.1033	-5.4932	-6.7072
8	0.0375	-0.0324	-0.0287	0.0241	0.0069	0.035	0.2218	0.5964	-0.1746	-0.0599	-0.0379	-0.1597	-0.3021	-0.3237	0	0.259	0.0974	0.0234	0.2215	0.0021	0.1547	48.9701	1.74	-13.2237
9	0.0687	-0.0439	-0.0033	0.1122	-0.1154	0.1876	0.1416	0.1923	0.1501	0.0499	-0.1545	-0.096	-0.2216	0.2367	0.0125	0.2317	0.0289	-0.0505	0.2399	-0.0078	0.2163	53.5024	-1.2203	-2.7476
10	0.0564	0.0323	0.015	0.1538	0.0314	0.0451	0.0894	-0.1235	-0.0771	0.3435	-0.1411	-0.1177	0.148	-0.0101	-0.0097	0.2038	0.0486	0.0096	0.1248	0.0038	0.1172	46.6334	-3.7043	6.2837
11	2.99	1.352	-0.0349	7.6161	1.9963	4.2366	0.0235	0.1911	0.3346	0.1974	-0.2288	0.1785	-0.0833	-0.2578	0.2179	0.252	0.1557	-0.0245	0.2454	0.0481	0.1577	35.2373	15.2727	-2.8806
12	3.4282	-0.3148	1.7739	4.8643	2.274	4.6234	0.0259	-0.0209	0.1371	-0.6172	-0.1324	-0.3013	-0.3892	0.1463	0.1343	0.3887	0.1781	0.0144	0.2563	0.0483	0.2275	39.8561	20.2874	-8.847
13	2.5183	-1.0768	-0.6972	4.334	-0.3881	1.5144	-0.0446	-0.036	0.1698	0.2931	0.0351	0.2218	-0.5196	-0.4788	0.0385	0.2867	0.1332	-0.01	0.2438	0.0106	0.1899	32.3871	15.3197	3.0505
14	6.6681	-1.0877	-5.2723	6.9424	2.5653	7.7283	-0.5185	-0.8045	0.1557	1.136	0.464	-0.7882	0.3475	0.7056	0.0482	0.5025	0.1505	-0.0926	0.2563	-0.0425	0.2835	43.0972	18.1545	10.0423
15	7.8913	1.4718	1.2207	7.3425	-2.333	4.8912	-0.2049	-0.8132	-0.4986	0.6968	0.257	0.1422	-0.1798	-0.4456	-0.1024	0.3026	0.1267	0.0126	0.2077	0.0326	0.2052	34.7326	7.6986	10.6114
16	9.0394	2.903	-3.1772	2.2989	-2.8008	3.7039	-0.0255	-0.6044	0.3266	0.2226	-0.4272	-0.457	-0.1294	0.7615	0.4512	0.3503	0.0759	-0.049	0.2701	-0.0232	0.31	47.3984	10.9198	4.4925
17	4.8142	4.2414	-4.9866	3.944	-3.9597	6.7069	0.1454	-0.656	-0.1577	0.3337	-0.3166	-0.6751	-0.1409	0.2814	0.1648	0.2446	0.025	-0.0237	0.2019	0.0088	0.2629	49.3554	5.004	10.5452
18	8.4037	3.3337	-1.1387	2.599	-2.9407	5.7184	-0.3145	0.6438	0.0277	-0.3176	0.1448	-0.1296	0.0539	0.2881	0.1411	0.3223	0.0454	-0.0012	0.201	0.0069	0.2127	47.5976	9.6109	-0.1247
19	2.1185	3.1503	-0.152	7.2189	-0.0385	4.4422	0.0346	0.4917	-0.1668	-0.1171	0.0336	-0.0695	0.1092	-0.2619	-0.037	0.2837	0.1624	-0.0511	0.2758	-0.0377	0.231	40.9826	4.3314	-7.5756

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 39 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 40 through 57 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 58 through 65 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 66 through 76 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 77 through 89 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 90 through 99 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 100 through 110 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 111 through 125 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 6 through 16 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 17 through 30 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 31 through 57 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 58 through 65 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 66 through 79 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 80 through 89 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 90 through 99 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 100 through 110 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 111 through 125 )

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