PDB-7wlv: Crystal Structure of the Multidrug effulx transporter BpeF from B...

ID or keywords:

Entry

Database: PDB / ID: 7wlv

Title

Crystal Structure of the Multidrug effulx transporter BpeF from Burkholderia pseudomallei.

Components

Efflux pump membrane transporter

Keywords

MEMBRANE PROTEIN / TRANSPORT PROTEIN

Function / homology

Function and homology information

xenobiotic transport / efflux transmembrane transporter activity / plasma membrane
Similarity search - Function

Biological species

Burkholderia pseudomallei K96243 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Kato, T. / Hung, L.-W. / Yamashita, E. / Okada, U. / Terwilliger, T.C. / Murakami, S.

Funding support

Japan, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism.
Authors: Kato, T. / Okada, U. / Hung, L.W. / Yamashita, E. / Kim, H.B. / Kim, C.Y. / Terwilliger, T.C. / Schweizer, H.P. / Murakami, S.

History

Deposition	Jan 13, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model Item: _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wlv.cif.gz	2.3 MB	Display	PDBx/mmCIF format
PDB format	pdb7wlv.ent.gz	2 MB	Display	PDB format
PDBx/mmJSON format	7wlv.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/wl/7wlv ftp://data.pdbj.org/pub/pdb/validation_reports/wl/7wlv	HTTPS FTP

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Related structure data

Related structure data	7wlsC 4dx5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	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	#95 - Nov 2007 Multidrug Resistance Transporters similarity (4) #96 - Dec 2007 Oxidosqualene Cyclase similarity (2)

Deposited unit

A: Efflux pump membrane transporter

B: Efflux pump membrane transporter

C: Efflux pump membrane transporter

D: Efflux pump membrane transporter

E: Efflux pump membrane transporter

F: Efflux pump membrane transporter

hetero molecules

695 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Efflux pump membrane transporter

B: Efflux pump membrane transporter

C: Efflux pump membrane transporter

hetero molecules

defined by author&software
Evidence: gel filtration
348 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Efflux pump membrane transporter

E: Efflux pump membrane transporter

F: Efflux pump membrane transporter

hetero molecules

defined by author&software
347 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.875, 121.141, 159.745
Angle α, β, γ (deg.)	97.39, 111.19, 100.60
Int Tables number	1
Space group name H-M	P1

#1: Protein	Efflux pump membrane transporter / Multidrug efflux transporter BpeF Mass: 115255.438 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria) Strain: K96243 / Gene: BPSS0293 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63NK6
#2: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 59.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 50mM N-(2-Acetamido)iminodiacetic acid, 100mM Lithium Chloride, 200mM Ammonium Sulfate, 36% PEG 300

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 3→49.02 Å / Num. obs: 160880 / % possible obs: 99.47 % / Redundancy: 5.3 % / CC_1/2: 0.997 / R_merge(I) obs: 0.094 / Net I/σ(I): 8.5
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 1.84 % / R_merge(I) obs: 0.661 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7513 / CC_1/2: 0.608 / % possible all: 93.07

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
XDS		data reduction
PHENIX	(1.20_4459: ???)	phasing
Coot		model building
MolProbity		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4DX5

4dx5

Resolution: 3→49.02 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 31.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2588	7874	4.91 %
R_work	0.211	-	-
obs	0.2133	160486	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3→49.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47539	0	245	41	47825

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	48703
X-RAY DIFFRACTION	f_angle_d	1.263	66292
X-RAY DIFFRACTION	f_dihedral_angle_d	14.693	17662
X-RAY DIFFRACTION	f_chiral_restr	0.069	7950
X-RAY DIFFRACTION	f_plane_restr	0.009	8468

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 (%)
3-3.03	0.4891	260	0.4285	4978	X-RAY DIFFRACTION	97
3.03-3.07	0.4255	246	0.3936	4977	X-RAY DIFFRACTION	98
3.07-3.11	0.3854	287	0.3586	4986	X-RAY DIFFRACTION	98
3.11-3.15	0.3956	255	0.3181	5103	X-RAY DIFFRACTION	100
3.15-3.19	0.3825	277	0.3012	5089	X-RAY DIFFRACTION	100
3.19-3.23	0.3585	254	0.2866	5133	X-RAY DIFFRACTION	100
3.23-3.28	0.3357	267	0.2672	5078	X-RAY DIFFRACTION	100
3.28-3.33	0.3144	258	0.256	5136	X-RAY DIFFRACTION	100
3.33-3.38	0.3345	253	0.2636	5065	X-RAY DIFFRACTION	100
3.38-3.43	0.3223	269	0.2649	5147	X-RAY DIFFRACTION	100
3.43-3.49	0.3325	278	0.2703	5048	X-RAY DIFFRACTION	100
3.49-3.56	0.3638	252	0.2704	5120	X-RAY DIFFRACTION	100
3.56-3.63	0.2735	237	0.2566	5117	X-RAY DIFFRACTION	100
3.63-3.7	0.3063	251	0.2422	5116	X-RAY DIFFRACTION	100
3.7-3.78	0.2659	238	0.2277	5161	X-RAY DIFFRACTION	100
3.78-3.87	0.2831	267	0.2072	5089	X-RAY DIFFRACTION	100
3.87-3.96	0.2857	258	0.2057	5076	X-RAY DIFFRACTION	100
3.96-4.07	0.2492	259	0.198	5101	X-RAY DIFFRACTION	100
4.07-4.19	0.2373	275	0.2018	5093	X-RAY DIFFRACTION	100
4.19-4.33	0.2366	261	0.1871	5099	X-RAY DIFFRACTION	100
4.33-4.48	0.242	297	0.179	5068	X-RAY DIFFRACTION	100
4.48-4.66	0.2217	270	0.1759	5101	X-RAY DIFFRACTION	100
4.66-4.87	0.2321	294	0.1711	5081	X-RAY DIFFRACTION	100
4.87-5.13	0.2264	270	0.1747	5082	X-RAY DIFFRACTION	100
5.13-5.45	0.2395	232	0.1877	5141	X-RAY DIFFRACTION	100
5.45-5.87	0.2607	286	0.2096	5056	X-RAY DIFFRACTION	100
5.87-6.46	0.2678	263	0.2171	5126	X-RAY DIFFRACTION	100
6.46-7.39	0.2466	239	0.1921	5106	X-RAY DIFFRACTION	100
7.39-9.3	0.1842	255	0.1493	5136	X-RAY DIFFRACTION	100
9.31-49.02	0.2457	266	0.2333	5003	X-RAY DIFFRACTION	99

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	2.8783	-0.5283	0.1602	1.0556	0.3277	1.8895	-0.4978	0.3491	0.4427	0.4244	0.1533	-0.0719	-0.38	-0.2353	-0.1224	0.7895	-0.1035	0.1816	0.7935	0.0074	0.699	-25.3749	48.4775	47.2295
2	0.2508	-0.1743	0.7578	0.5663	-0.5472	1.893	-0.0927	0.018	0.3289	-0.0659	-0.0325	-0.2359	-0.2111	-0.1506	-0.0004	1.0189	0.0788	0.1689	0.9955	0.0934	1.0754	-19.4934	59.4047	49.0647
3	0.6947	0.5064	-0.519	1.2861	-0.2834	0.4911	0.2432	-0.3987	-0.2708	0.1765	-0.2305	-0.377	0.1257	0.7297	-0.0068	0.7276	0.0723	0.1088	0.7176	-0.0726	0.4382	0.6169	27.8212	70.1004
4	0.2537	-0.209	-0.1949	0.6796	-0.2236	0.1456	-0.1151	-0.1522	-0.0912	0.2451	0.2172	0.2125	-0.1189	-0.1948	-0.0003	1.568	0.455	0.0135	1.398	-0.0883	0.9939	-12.3539	34.3877	85.7746
5	2.1397	-0.3495	-0.1332	1.8391	0.1671	1.1037	-0.3273	-0.1652	-0.0472	0.5389	0.3514	0.2865	-0.1939	-0.6238	0.0005	1.0517	0.2014	0.2256	1.2174	0.1368	0.8946	-46.1165	56.8901	54.0402
6	1.0971	0.6884	-0.1188	0.5122	-0.3528	1.1934	0.1371	-0.5498	0.4948	0.5679	0.2717	0.6194	-1.1976	-0.8769	-0.0059	0.8363	0.0884	0.1591	0.9134	0.1085	0.869	-17.3123	21.0897	75.8586
7	1.7055	1.1197	-0.1927	0.7433	0.1612	1.7157	0.0526	-0.2706	-0.5195	-0.179	0.1662	0.3343	0.1112	-0.0013	0.0012	0.9498	0.1354	0.0458	1.0365	0.0238	0.8332	-7.5387	25.037	83.4256
8	1.412	-1.0992	0.2111	0.7235	-0.3162	0.3998	0.2792	0.3905	-0.097	-0.1701	-0.0498	0.197	0.0447	-0.0765	0	1.0277	-0.0722	-0.0533	0.9964	0.025	1.0383	-17.3318	45.053	13.8292
9	0.481	0.5878	0.4837	0.706	0.5372	3.501	0.018	0.2868	0.0013	-0.3749	0.0675	0.3075	-0.1181	0.4593	0.0001	0.6294	-0.0779	-0.0017	0.7652	0.0341	0.8356	17.7901	25.1725	37.4471
10	-0.1061	0.0815	0.4418	0.1896	0.8191	3.1165	0.1427	0.4399	0.0885	0.2967	0.1443	-0.3153	0.5426	1.2802	0.0824	0.7748	-0.0749	0.1076	1.2885	0.1676	1.0037	30.3789	36.4187	30.9632
11	2.1739	-0.4584	0.5301	0.9685	0.02	0.3134	-0.0327	0.1433	0.4132	0.2433	-0.0807	-0.1394	-0.4037	-0.0592	-0.0006	1.1838	-0.0497	0.0503	0.9634	0.2043	1.0364	-11.0505	66.7404	14.6419
12	1.307	-0.0923	-0.399	0.635	0.4172	0.34	-0.0588	0.6863	0.1101	0.0343	0.4474	0.1499	-0.4215	-0.8292	-0.001	0.8537	-0.0464	-0.0103	0.9869	-0.0247	0.7925	21.5526	43.4565	45.5414
13	1.8945	-2.0197	-0.8142	2.6409	1.1378	0.3798	0.3645	1.0385	0.0388	-0.7632	-0.5078	-0.0417	0.1281	0.5536	0.0002	0.6356	0.0164	0.0315	1.0516	0.1631	0.8356	30.5056	35.3398	40.0401
14	0.7095	-0.5807	0.8162	0.6903	-0.6735	0.2791	0.0262	-0.2181	-0.3076	0.0308	0.251	0.4733	0.0528	-0.1609	0.0005	0.9282	-0.0108	-0.0194	1.0963	0.1243	1.1048	-44.1496	34.1904	31.4557
15	2.8408	-0.4065	-0.7497	0.873	-0.8258	1.453	-0.13	-0.2435	-0.4059	-0.0265	0.153	0.4776	0.305	-0.17	-0.0004	0.8022	-0.0698	-0.2283	0.5784	-0.1735	0.8602	-12.1062	-5.2582	48.2653
16	0.3485	0.1603	-0.3432	0.9012	-0.2182	0.2414	0.2346	0.4905	-0.3931	-0.5843	0.1632	0.7949	0.4069	-0.2138	-0.0001	1.2607	-0.1155	-0.449	1.1343	0.0237	1.5615	-36.9012	6.999	20.2259
17	2.646	-1.7956	1.1342	1.2079	-0.644	0.5963	0.364	0.8623	-0.438	-0.2736	-0.5431	-0.3042	-0.2525	0.7516	0.0167	1.0453	-0.118	-0.3661	0.782	-0.1091	1.3526	-45.289	5.8375	22.6277
18	2.363	-0.0274	-0.279	0.756	1.0039	3.4079	0.391	0.6808	-0.5802	-0.8779	-0.0206	0.28	0.3527	0.1857	0.0107	1.3778	0.0471	-0.196	1.1835	-0.047	1.2339	-42.8143	31.5594	6.2192
19	7.0291	0.5874	4.9025	1.974	1.7318	5.9736	1.7012	0.5233	-2.0279	0.8947	-0.6006	0.5734	1.8658	-0.2262	0.587	0.9122	0.2363	-0.1432	0.8242	-0.311	0.6284	-4.7198	-0.1461	27.6266
20	0.6352	0.7909	-0.3572	1.0902	0.0559	1.2206	0.2086	0.0218	0.0854	-0.1265	-0.2059	0.305	0.0625	0.0616	0.0005	1.027	0.0079	-0.2967	0.7494	-0.1543	0.8051	-6.4959	-10.2249	36.3395
21	0.6097	-0.1914	0.144	0.4712	-0.1297	0.7089	-0.0395	0.1203	0.3314	-0.1182	-0.2527	-0.3489	-0.0036	0.179	-0.0005	0.8518	-0.0101	0.0873	0.8634	-0.0498	0.9769	2.4471	8.7215	-63.2985
22	1.9964	-0.3476	-0.3959	2.0023	1.47	1.2858	0.3677	0.1548	-0.2662	-0.2415	-0.4104	0.2007	0.6009	-0.0117	0.0192	1.066	0.1191	0.0984	0.9271	-0.0746	0.9008	14.3005	-18.4794	-59.4743
23	3.3796	-0.453	0.2332	3.3098	-0.815	2.6221	0.8958	1.1613	-0.0487	-0.8689	-0.5944	-0.0177	-0.2446	0.1601	0.137	0.9182	0.102	-0.1023	0.7192	-0.2692	0.5778	-24.5406	10.6667	-86.6463
24	0.7396	-1.0252	0.4247	1.448	-0.3973	0.8027	-0.1682	-0.4211	-0.1178	0.4271	0.3598	-0.0901	-0.0708	-0.0626	0	1.0042	-0.0305	-0.0186	0.9192	-0.067	0.9693	-2.7673	16.5996	-23.3913
25	0.2986	0.2938	0.8258	0.9691	-0.3435	2.8953	-0.0847	-0.1104	0.1597	0.1765	0.0852	-0.0128	-0.5207	-0.0387	-0.0023	0.8485	-0.0542	0.0408	0.5352	-0.1943	0.6196	-8.5804	44.8308	-34.3137
26	1.6391	-0.2853	-0.8149	0.4637	0.3845	1.5205	-0.2103	-0.3047	-0.0283	0.4882	-0.037	-0.5295	0.0727	0.1856	0.0004	0.8416	-0.0802	-0.2618	1.0054	-0.1111	1.0525	26.2499	12.5861	-21.271
27	0.5664	0.0529	0.1726	0.6309	0.5094	0.5495	-0.2667	-0.2138	0.135	0.2428	0.1589	-0.4108	-0.0852	0.1333	-0.0007	0.6877	-0.1388	0.0513	0.8385	-0.0226	0.9955	15.5609	27.6526	-42.7446
28	2.8116	-1.3117	-1.2379	0.8484	0.3684	0.5132	-0.1718	-0.5365	0.3028	0.1543	-0.1484	-0.4442	-0.4902	0.4677	-0.0006	1.1582	-0.0947	-0.0493	0.8814	-0.0555	1.0542	-13.1901	55.648	-49.1572
29	0.2792	0.0633	-0.153	1.2576	-0.7196	0.5743	0.2345	-0.219	-0.5091	-0.169	-0.1536	0.1125	0.135	0.233	-0.0005	1.2191	-0.0195	0.0081	1.0405	0.0115	0.9745	-7.5208	-17.4923	-35.855
30	1.2507	-0.2024	-0.3426	1.2321	0.6903	1.1026	0.0886	-0.1797	-0.7228	0.0922	0.0758	0.5224	0.0113	-0.283	0.0018	0.5952	-0.0551	0.0549	0.6214	0.1332	0.7855	-51.1581	8.3233	-52.1848
31	0.1812	-0.5701	-0.117	1.2741	-0.0735	-0.069	0.0899	-0.0522	-0.1184	0.548	0.1161	0.1859	0.0529	0.2697	0.1707	1.1857	-0.0502	0.2426	1.0246	0.306	1.2367	-32.2606	-14.4263	-20.7365
32	0.958	-0.6658	0.0975	1.8338	-0.7965	1.8482	-0.6207	-0.7063	-0.3193	0.8066	0.6045	0.1539	-0.2745	-0.2377	0.0024	0.9586	-0.045	0.099	0.9722	0.13	0.7986	-21.6285	-5.6931	-20.5325
33	0.3027	0.4787	0.7577	0.7328	0.4586	1.903	0.0646	-0.1095	0.2395	-0.3844	0.3	0.8362	-0.3272	-0.5702	0.0033	0.5419	-0.1319	0.2537	0.8964	0.1965	0.6525	-57.5576	12.8418	-39.319

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 163 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 164 through 428 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 429 through 507 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 508 through 591 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 592 through 880 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 881 through 932 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 933 through 1042 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 361 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 362 through 498 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 499 through 591 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 592 through 879 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 880 through 932 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 933 through 1042 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 331 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 332 through 544 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 545 through 631 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 632 through 687 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 688 through 878 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 879 through 932 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 933 through 1043 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 591 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 592 through 880 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 881 through 1042 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 2 through 428 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 429 through 665 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 666 through 804 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 805 through 904 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 905 through 1043 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 1 through 331 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 332 through 544 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 545 through 716 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 717 through 963 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 964 through 1043 )

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