PDB-7wls: Crystal structure of the multidrug efflux transporter BpeB from B...

ID or keywords:

Entry

Database: PDB / ID: 7wls

Title

Crystal structure of the multidrug efflux transporter BpeB from Burkholderia pseudomallei

Components

Efflux pump membrane transporter

Keywords

MEMBRANE PROTEIN / TRANSPORT PROTEIN

Function / homology

Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / xenobiotic transport / efflux transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter

Function and homology information

Biological species

Burkholderia pseudomallei K96243 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.94 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	7wls.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb7wls.ent.gz	981.6 KB	Display	PDB format
PDBx/mmJSON format	7wls.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wls_validation.pdf.gz	951.8 KB	Display	wwPDB validaton report
Full document	7wls_full_validation.pdf.gz	1015.7 KB	Display
Data in XML	7wls_validation.xml.gz	103.9 KB	Display
Data in CIF	7wls_validation.cif.gz	140.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/7wls ftp://data.pdbj.org/pub/pdb/validation_reports/wl/7wls	HTTPS FTP

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Related structure data

Related structure data	7wlvC 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)

Deposited unit

A: Efflux pump membrane transporter

B: Efflux pump membrane transporter

C: Efflux pump membrane transporter

hetero molecules

341 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	207.883, 135.977, 157.819
Angle α, β, γ (deg.)	90.000, 98.210, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Efflux pump membrane transporter / Multidrug efflux transporter BpeB Mass: 113236.508 Da / Num. of mol.: 3 / Mutation: deletions A1046-D1066 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria) Strain: K96243 / Gene: bpeB, BPSL0815 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63WS7
#2: Chemical	ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE Mass: 496.589 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₃H₄₄O₁₁ / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.15 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 50mM 2-Morpholinoethanesulfonate 200mM Sodium Chloride 21% PEG 2000

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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 30, 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: 2.94→48.8 Å / Num. obs: 92277 / % possible obs: 99.45 % / Redundancy: 3.7 % / B_iso Wilson estimate: 98.3 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.089 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.94→2.99 Å / R_merge(I) obs: 1.128 / Mean I/σ(I) obs: 1 / Num. unique obs: 4438 / CC_1/2: 0.622

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Processing

Software

Name	Version	Classification
PHENIX	1.20rc1_4387	refinement
XDS		data reduction
PHENIX	1.20rc1_4387	phasing
Coot		model building
MolProbity		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4DX5

4dx5

Resolution: 2.94→48.8 Å / SU ML: 0.4852 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.6189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2844	4612	5 %
R_work	0.2298	87553	-
obs	0.2326	92165	99.33 %

Solvent computation

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

Displacement parameters

B_iso mean: 122.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.94→48.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23135	0	115	0	23250

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0108	23713
X-RAY DIFFRACTION	f_angle_d	1.319	32284
X-RAY DIFFRACTION	f_chiral_restr	0.0743	3881
X-RAY DIFFRACTION	f_plane_restr	0.01	4088
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8919	8469

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 (%)
2.94-2.97	0.5811	152	0.5581	2736	X-RAY DIFFRACTION	94.56
2.97-3	0.5291	143	0.4678	2905	X-RAY DIFFRACTION	99.74
3-3.04	0.4832	117	0.4015	2983	X-RAY DIFFRACTION	99.68
3.04-3.08	0.4274	158	0.3649	2877	X-RAY DIFFRACTION	99.51
3.08-3.12	0.3698	152	0.3303	2925	X-RAY DIFFRACTION	99.74
3.12-3.16	0.3643	151	0.3171	2972	X-RAY DIFFRACTION	99.84
3.16-3.21	0.3611	153	0.3215	2897	X-RAY DIFFRACTION	99.74
3.21-3.26	0.3947	145	0.3283	2937	X-RAY DIFFRACTION	99.87
3.26-3.31	0.3923	148	0.326	2912	X-RAY DIFFRACTION	99.74
3.31-3.36	0.3477	169	0.2972	2948	X-RAY DIFFRACTION	99.9
3.36-3.42	0.3039	149	0.2662	2911	X-RAY DIFFRACTION	99.8
3.42-3.48	0.3648	165	0.25	2872	X-RAY DIFFRACTION	99.74
3.48-3.55	0.3078	163	0.2602	2925	X-RAY DIFFRACTION	99.65
3.55-3.62	0.336	144	0.2445	2916	X-RAY DIFFRACTION	99.67
3.62-3.7	0.2925	155	0.2415	2931	X-RAY DIFFRACTION	99.71
3.7-3.79	0.3242	188	0.2371	2916	X-RAY DIFFRACTION	99.68
3.79-3.88	0.2627	126	0.243	2939	X-RAY DIFFRACTION	99.71
3.88-3.98	0.286	174	0.2436	2889	X-RAY DIFFRACTION	99.71
3.98-4.1	0.3086	173	0.2299	2912	X-RAY DIFFRACTION	99.68
4.1-4.23	0.294	182	0.2173	2885	X-RAY DIFFRACTION	99.42
4.23-4.39	0.2918	141	0.2091	2926	X-RAY DIFFRACTION	99.26
4.39-4.56	0.2162	128	0.1871	2959	X-RAY DIFFRACTION	99.58
4.56-4.77	0.2204	129	0.1826	2959	X-RAY DIFFRACTION	99.61
4.77-5.02	0.2176	160	0.1715	2895	X-RAY DIFFRACTION	99.09
5.02-5.33	0.2397	173	0.1933	2927	X-RAY DIFFRACTION	99.36
5.33-5.74	0.2918	142	0.2155	2917	X-RAY DIFFRACTION	99.22
5.74-6.32	0.2745	148	0.2292	2955	X-RAY DIFFRACTION	99.39
6.32-7.23	0.2852	170	0.2148	2922	X-RAY DIFFRACTION	99.29
7.23-9.1	0.2108	170	0.1788	2935	X-RAY DIFFRACTION	98.82
9.1-48.8	0.2834	144	0.231	2970	X-RAY DIFFRACTION	97.31

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	0.570703632416	0.684042699926	-0.00692274477388	1.42744610576	-0.448367542677	0.715525619007	0.141797840826	-0.119534789962	-0.154319682764	0.221035939381	-0.216964628425	0.0201752983982	-0.194222201066	0.134609318284	0.000195907414001	0.803384178631	-0.0359373069807	-0.124561995938	0.741316261051	0.0738532054887	0.641197292313	-44.8901066308	31.988514594	64.5190491413
2	0.245320065776	0.169267849886	0.225650048864	0.0316778945445	0.10116331981	0.996313921456	-0.283428771202	0.120534103294	-0.623985844628	-0.509782420879	-0.0895468064444	-0.149179271054	0.502782723518	0.242885420979	-0.000720588703626	0.887193225648	0.174442467094	0.14469307614	1.08070026301	0.181734607298	1.35144274341	-5.26489381974	24.1543282828	37.4188843218
3	0.0905602899294	-1.49775265434	-1.54834320967	0.341838836938	0.940382192021	0.0961245537929	0.203097811167	-0.565754922882	-0.166764487889	-0.0534796894251	-0.138908825907	-0.130299050068	-0.246688629108	0.0879101362334	-0.117659440903	1.06218096688	0.12173081211	0.0848943091664	1.32009104408	0.367827211811	1.57464558079	-22.0335848349	9.00595864447	63.7879892078
4	0.326165651429	-0.401571730446	-0.794727145815	0.733656555435	0.617891184551	1.94584444569	-0.51541829809	-0.265942558219	-0.390050217429	0.0964932910785	0.155614512524	0.431365736497	0.450993236695	-0.0895777642492	0.000593577866299	1.11333588098	-0.057734014102	0.067224171045	0.908597532164	0.133119307678	1.08068356741	-62.8928210886	14.4701177874	73.0712437109
5	2.4687875793	1.99594601559	-3.52715989284	1.28651461896	-2.43109869268	7.74022067283	-0.872450116584	-1.47423648554	-2.50601910626	1.03497838924	-0.592072985471	-0.0552011440423	0.833175902887	2.17412888957	-0.258323122129	1.70365943505	0.0749984372605	0.876975526199	0.790854497661	0.0307729367805	2.3150742957	-32.6097466437	3.0157746364	47.3404865288
6	1.62105151403	0.43827292201	0.136930009042	0.317565397291	0.306033233833	0.189147746875	0.236618907565	-0.184793435772	-0.438478367724	-0.0724554258309	-0.305100186069	0.151772842498	0.188439153873	0.423228329517	-0.000136157554016	1.22228344436	0.388063357581	0.388159144366	1.38259626367	0.299352344446	1.74219497094	-3.68148561421	6.22820000086	39.2359358732
7	1.93122017907	0.234527630867	-1.83910008212	0.669836580547	-0.236852849458	1.93077693374	0.222356306072	0.116077860097	0.477659000388	0.228008674443	0.119832453966	0.313580079007	-0.268224268586	-0.181816199302	0.00186199989433	0.708985907557	-0.0224311231015	-0.141792294628	0.636903900691	0.0639901866741	0.771804028462	-63.3143793841	47.9811105999	45.5741457685
8	1.17623172561	-0.117166984543	0.45071973817	1.96390341504	-0.258260830074	0.996608314731	0.0400757305053	0.26549257955	0.204533992218	-0.363608174741	-0.170976693484	0.0763471589784	0.158090705287	0.034588128272	-0.00747284043947	1.04509515818	0.102608422458	-0.103479287468	0.830426009087	0.225062912512	0.8365935123	-52.3165258422	63.7409396136	29.8611559608
9	-0.0155033987534	-0.484637685412	-0.0617622272002	2.43055806834	0.279365087341	0.533653969207	-0.147466466478	0.339235367229	-0.0699684136414	-0.277833609836	-0.0408362153263	-0.22087067364	0.1151964702	0.131908144652	2.68352574013E-5	0.874424011445	-0.0957357063706	0.254977743173	1.06073411644	0.151079846783	0.906575101533	-15.3012118103	58.9826802031	19.8927513283
10	1.49538139394	-0.369821461655	-0.185811146751	-0.0973218383835	-0.772380897315	-0.272525324726	0.663343690025	-0.00406674546932	1.54453335556	0.434707057867	0.0557898659346	0.0797745378789	-0.416244754519	0.20035197273	0.0594713711568	1.36610668493	-0.153515947308	0.362853302177	1.02493142103	-0.0235389973448	1.52852432976	-44.2063615372	75.0747281626	45.197018967
11	1.20344254866	-0.24021329364	-0.584437118236	0.587060919001	-0.278606579959	1.45327141765	0.465223022151	-0.384367074694	0.516740608921	0.201816246361	-0.0914359263927	0.113854103956	-0.558873809357	0.328400958248	-0.000198006893857	1.15070259298	-0.106088046906	0.0327976512183	0.832921224429	-0.17258589001	1.05873203254	-56.8340281692	59.1137407923	65.7422816585
12	0.961568376089	0.207842239455	-0.474202440497	1.05851331492	-0.229041083491	1.23294798587	0.18734541313	0.0842577975181	0.489480797303	-0.286926736612	0.0738327803186	0.166775526597	-0.521883128026	0.172408093336	0.000306117778472	0.84192458391	-0.168868038742	-0.0372052143977	0.997674914455	0.00751975689772	0.834970084593	-10.1933820391	63.4327755341	32.2285635725
13	1.3281888947	0.147096142179	-0.912677600476	0.522687019959	-0.273911090833	1.36292678273	-0.396108355425	0.265485093239	-0.484148900051	-0.0085161492614	0.0580696345515	0.098305126826	0.403238183332	-0.328728339262	-0.000715574784534	0.818084519529	-0.179680708052	-0.103775818149	0.836360775	-0.17015461505	0.845598796175	-61.6240816718	17.9661697677	38.9287446339
14	1.23052425059	-0.191362773935	0.934160265612	1.57838285867	-0.115148337824	0.508287667595	-0.386009962764	1.19246699	-0.262145984789	-1.92559717687	-0.312863053038	-0.599631725018	1.09124581481	0.0630745713092	-0.418257432318	1.65236095323	0.0311463626249	0.559920806194	1.37431354453	-0.172866716357	1.0543968326	-25.498861275	17.8973891512	3.41553238638
15	1.46688531092	0.927787191569	-1.58542154776	0.47800991558	-0.653766902713	2.34635526119	-0.491994060331	0.702960811547	-0.402889600062	-0.279720679478	0.176056806419	-0.0200369534819	0.360039877653	-0.781968043281	-0.000503165216471	0.951370177059	-0.239611256195	-0.105743305641	1.18379615421	-0.180117481627	0.975537325888	-75.2484449266	24.6691405336	23.483222878
16	0.144481580932	0.572659964986	-0.626700829734	4.8021571056	-0.4759504917	1.02201522406	-0.42447790053	0.985277482469	-1.56900130222	-0.229605331061	-0.352041440776	-1.58574264442	1.01420339132	-0.392148375546	-0.815289785435	1.13548359737	-0.489215159198	0.153172052286	1.60781022793	-0.441665300477	0.370583549741	-34.2601274245	27.8534966304	-2.87474191201

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 359 )	A	A	1 - 359	1 - 359
2	2	chain 'A' and (resid 360 through 496 )	A	A	360 - 496	360 - 496
3	3	chain 'A' and (resid 497 through 678 )	A	A	497 - 678	497 - 665
4	4	chain 'A' and (resid 679 through 820 )	A	A	679 - 820	666 - 807
5	5	chain 'A' and (resid 821 through 891 )	A	A	821 - 891	808 - 878
6	6	chain 'A' and (resid 892 through 1032 )	A	A	892 - 1032	879 - 1019
7	7	chain 'B' and (resid 1 through 265 )	B	B	1 - 265	1 - 265
8	8	chain 'B' and (resid 266 through 359 )	B	B	266 - 359	266 - 359
9	9	chain 'B' and (resid 360 through 535 )	B	B	360 - 535	360 - 526
10	10	chain 'B' and (resid 536 through 655 )	B	B	536 - 655	527 - 646
11	11	chain 'B' and (resid 656 through 868 )	B	B	656 - 868	647 - 859
12	12	chain 'B' and (resid 869 through 1033 )	B	B	869 - 1033	860 - 1024
13	13	chain 'C' and (resid 1 through 359 )	C	C	1 - 359	1 - 359
14	14	chain 'C' and (resid 360 through 535 )	C	C	360 - 535	360 - 519
15	15	chain 'C' and (resid 536 through 860 )	C	C	536 - 860	520 - 844
16	16	chain 'C' and (resid 861 through 1034 )	C	C	861 - 1034	845 - 1018

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