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

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Basic information

Entry
Database: PDB / ID: 7wlv
TitleCrystal Structure of the Multidrug effulx transporter BpeF from Burkholderia pseudomallei.
ComponentsEfflux pump membrane transporter
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


xenobiotic transport / efflux transmembrane transporter activity / plasma membrane
Similarity search - Function
Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Efflux pump membrane transporter
Similarity search - Component
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKato, T. / Hung, L.-W. / Yamashita, E. / Okada, U. / Terwilliger, T.C. / Murakami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02412 Japan
CitationJournal: 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
DepositionJan 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)695,10713
Polymers691,5336
Non-polymers3,5747
Water73941
1
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,8097
Polymers345,7663
Non-polymers2,0424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21790 Å2
ΔGint-58 kcal/mol
Surface area119280 Å2
MethodPISA
2
D: Efflux pump membrane transporter
E: Efflux pump membrane transporter
F: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,2986
Polymers345,7663
Non-polymers1,5323
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18310 Å2
ΔGint-68 kcal/mol
Surface area119640 Å2
MethodPISA
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 number1
Space group name H-MP1

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Components

#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 interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→49.02 Å / Num. obs: 160880 / % possible obs: 99.47 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7513 / CC1/2: 0.608 / % possible all: 93.07

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
PHENIX(1.20_4459: ???)phasing
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 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
RfactorNum. reflection% reflection
Rfree0.2588 7874 4.91 %
Rwork0.211 --
obs0.2133 160486 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47539 0 245 41 47825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00948703
X-RAY DIFFRACTIONf_angle_d1.26366292
X-RAY DIFFRACTIONf_dihedral_angle_d14.69317662
X-RAY DIFFRACTIONf_chiral_restr0.0697950
X-RAY DIFFRACTIONf_plane_restr0.0098468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.48912600.42854978X-RAY DIFFRACTION97
3.03-3.070.42552460.39364977X-RAY DIFFRACTION98
3.07-3.110.38542870.35864986X-RAY DIFFRACTION98
3.11-3.150.39562550.31815103X-RAY DIFFRACTION100
3.15-3.190.38252770.30125089X-RAY DIFFRACTION100
3.19-3.230.35852540.28665133X-RAY DIFFRACTION100
3.23-3.280.33572670.26725078X-RAY DIFFRACTION100
3.28-3.330.31442580.2565136X-RAY DIFFRACTION100
3.33-3.380.33452530.26365065X-RAY DIFFRACTION100
3.38-3.430.32232690.26495147X-RAY DIFFRACTION100
3.43-3.490.33252780.27035048X-RAY DIFFRACTION100
3.49-3.560.36382520.27045120X-RAY DIFFRACTION100
3.56-3.630.27352370.25665117X-RAY DIFFRACTION100
3.63-3.70.30632510.24225116X-RAY DIFFRACTION100
3.7-3.780.26592380.22775161X-RAY DIFFRACTION100
3.78-3.870.28312670.20725089X-RAY DIFFRACTION100
3.87-3.960.28572580.20575076X-RAY DIFFRACTION100
3.96-4.070.24922590.1985101X-RAY DIFFRACTION100
4.07-4.190.23732750.20185093X-RAY DIFFRACTION100
4.19-4.330.23662610.18715099X-RAY DIFFRACTION100
4.33-4.480.2422970.1795068X-RAY DIFFRACTION100
4.48-4.660.22172700.17595101X-RAY DIFFRACTION100
4.66-4.870.23212940.17115081X-RAY DIFFRACTION100
4.87-5.130.22642700.17475082X-RAY DIFFRACTION100
5.13-5.450.23952320.18775141X-RAY DIFFRACTION100
5.45-5.870.26072860.20965056X-RAY DIFFRACTION100
5.87-6.460.26782630.21715126X-RAY DIFFRACTION100
6.46-7.390.24662390.19215106X-RAY DIFFRACTION100
7.39-9.30.18422550.14935136X-RAY DIFFRACTION100
9.31-49.020.24572660.23335003X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8783-0.52830.16021.05560.32771.8895-0.49780.34910.44270.42440.1533-0.0719-0.38-0.2353-0.12240.7895-0.10350.18160.79350.00740.699-25.374948.477547.2295
20.2508-0.17430.75780.5663-0.54721.893-0.09270.0180.3289-0.0659-0.0325-0.2359-0.2111-0.1506-0.00041.01890.07880.16890.99550.09341.0754-19.493459.404749.0647
30.69470.5064-0.5191.2861-0.28340.49110.2432-0.3987-0.27080.1765-0.2305-0.3770.12570.7297-0.00680.72760.07230.10880.7176-0.07260.43820.616927.821270.1004
40.2537-0.209-0.19490.6796-0.22360.1456-0.1151-0.1522-0.09120.24510.21720.2125-0.1189-0.1948-0.00031.5680.4550.01351.398-0.08830.9939-12.353934.387785.7746
52.1397-0.3495-0.13321.83910.16711.1037-0.3273-0.1652-0.04720.53890.35140.2865-0.1939-0.62380.00051.05170.20140.22561.21740.13680.8946-46.116556.890154.0402
61.09710.6884-0.11880.5122-0.35281.19340.1371-0.54980.49480.56790.27170.6194-1.1976-0.8769-0.00590.83630.08840.15910.91340.10850.869-17.312321.089775.8586
71.70551.1197-0.19270.74330.16121.71570.0526-0.2706-0.5195-0.1790.16620.33430.1112-0.00130.00120.94980.13540.04581.03650.02380.8332-7.538725.03783.4256
81.412-1.09920.21110.7235-0.31620.39980.27920.3905-0.097-0.1701-0.04980.1970.0447-0.076501.0277-0.0722-0.05330.99640.0251.0383-17.331845.05313.8292
90.4810.58780.48370.7060.53723.5010.0180.28680.0013-0.37490.06750.3075-0.11810.45930.00010.6294-0.0779-0.00170.76520.03410.835617.790125.172537.4471
10-0.10610.08150.44180.18960.81913.11650.14270.43990.08850.29670.1443-0.31530.54261.28020.08240.7748-0.07490.10761.28850.16761.003730.378936.418730.9632
112.1739-0.45840.53010.96850.020.3134-0.03270.14330.41320.2433-0.0807-0.1394-0.4037-0.0592-0.00061.1838-0.04970.05030.96340.20431.0364-11.050566.740414.6419
121.307-0.0923-0.3990.6350.41720.34-0.05880.68630.11010.03430.44740.1499-0.4215-0.8292-0.0010.8537-0.0464-0.01030.9869-0.02470.792521.552643.456545.5414
131.8945-2.0197-0.81422.64091.13780.37980.36451.03850.0388-0.7632-0.5078-0.04170.12810.55360.00020.63560.01640.03151.05160.16310.835630.505635.339840.0401
140.7095-0.58070.81620.6903-0.67350.27910.0262-0.2181-0.30760.03080.2510.47330.0528-0.16090.00050.9282-0.0108-0.01941.09630.12431.1048-44.149634.190431.4557
152.8408-0.4065-0.74970.873-0.82581.453-0.13-0.2435-0.4059-0.02650.1530.47760.305-0.17-0.00040.8022-0.0698-0.22830.5784-0.17350.8602-12.1062-5.258248.2653
160.34850.1603-0.34320.9012-0.21820.24140.23460.4905-0.3931-0.58430.16320.79490.4069-0.2138-0.00011.2607-0.1155-0.4491.13430.02371.5615-36.90126.99920.2259
172.646-1.79561.13421.2079-0.6440.59630.3640.8623-0.438-0.2736-0.5431-0.3042-0.25250.75160.01671.0453-0.118-0.36610.782-0.10911.3526-45.2895.837522.6277
182.363-0.0274-0.2790.7561.00393.40790.3910.6808-0.5802-0.8779-0.02060.280.35270.18570.01071.37780.0471-0.1961.1835-0.0471.2339-42.814331.55946.2192
197.02910.58744.90251.9741.73185.97361.70120.5233-2.02790.8947-0.60060.57341.8658-0.22620.5870.91220.2363-0.14320.8242-0.3110.6284-4.7198-0.146127.6266
200.63520.7909-0.35721.09020.05591.22060.20860.02180.0854-0.1265-0.20590.3050.06250.06160.00051.0270.0079-0.29670.7494-0.15430.8051-6.4959-10.224936.3395
210.6097-0.19140.1440.4712-0.12970.7089-0.03950.12030.3314-0.1182-0.2527-0.3489-0.00360.179-0.00050.8518-0.01010.08730.8634-0.04980.97692.44718.7215-63.2985
221.9964-0.3476-0.39592.00231.471.28580.36770.1548-0.2662-0.2415-0.41040.20070.6009-0.01170.01921.0660.11910.09840.9271-0.07460.900814.3005-18.4794-59.4743
233.3796-0.4530.23323.3098-0.8152.62210.89581.1613-0.0487-0.8689-0.5944-0.0177-0.24460.16010.1370.91820.102-0.10230.7192-0.26920.5778-24.540610.6667-86.6463
240.7396-1.02520.42471.448-0.39730.8027-0.1682-0.4211-0.11780.42710.3598-0.0901-0.0708-0.062601.0042-0.0305-0.01860.9192-0.0670.9693-2.767316.5996-23.3913
250.29860.29380.82580.9691-0.34352.8953-0.0847-0.11040.15970.17650.0852-0.0128-0.5207-0.0387-0.00230.8485-0.05420.04080.5352-0.19430.6196-8.580444.8308-34.3137
261.6391-0.2853-0.81490.46370.38451.5205-0.2103-0.3047-0.02830.4882-0.037-0.52950.07270.18560.00040.8416-0.0802-0.26181.0054-0.11111.052526.249912.5861-21.271
270.56640.05290.17260.63090.50940.5495-0.2667-0.21380.1350.24280.1589-0.4108-0.08520.1333-0.00070.6877-0.13880.05130.8385-0.02260.995515.560927.6526-42.7446
282.8116-1.3117-1.23790.84840.36840.5132-0.1718-0.53650.30280.1543-0.1484-0.4442-0.49020.4677-0.00061.1582-0.0947-0.04930.8814-0.05551.0542-13.190155.648-49.1572
290.27920.0633-0.1531.2576-0.71960.57430.2345-0.219-0.5091-0.169-0.15360.11250.1350.233-0.00051.2191-0.01950.00811.04050.01150.9745-7.5208-17.4923-35.855
301.2507-0.2024-0.34261.23210.69031.10260.0886-0.1797-0.72280.09220.07580.52240.0113-0.2830.00180.5952-0.05510.05490.62140.13320.7855-51.15818.3233-52.1848
310.1812-0.5701-0.1171.2741-0.0735-0.0690.0899-0.0522-0.11840.5480.11610.18590.05290.26970.17071.1857-0.05020.24261.02460.3061.2367-32.2606-14.4263-20.7365
320.958-0.66580.09751.8338-0.79651.8482-0.6207-0.7063-0.31930.80660.60450.1539-0.2745-0.23770.00240.9586-0.0450.0990.97220.130.7986-21.6285-5.6931-20.5325
330.30270.47870.75770.73280.45861.9030.0646-0.10950.2395-0.38440.30.8362-0.3272-0.57020.00330.5419-0.13190.25370.89640.19650.6525-57.557612.8418-39.319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 163 )
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 428 )
3X-RAY DIFFRACTION3chain 'A' and (resid 429 through 507 )
4X-RAY DIFFRACTION4chain 'A' and (resid 508 through 591 )
5X-RAY DIFFRACTION5chain 'A' and (resid 592 through 880 )
6X-RAY DIFFRACTION6chain 'A' and (resid 881 through 932 )
7X-RAY DIFFRACTION7chain 'A' and (resid 933 through 1042 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 361 )
9X-RAY DIFFRACTION9chain 'B' and (resid 362 through 498 )
10X-RAY DIFFRACTION10chain 'B' and (resid 499 through 591 )
11X-RAY DIFFRACTION11chain 'B' and (resid 592 through 879 )
12X-RAY DIFFRACTION12chain 'B' and (resid 880 through 932 )
13X-RAY DIFFRACTION13chain 'B' and (resid 933 through 1042 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 331 )
15X-RAY DIFFRACTION15chain 'C' and (resid 332 through 544 )
16X-RAY DIFFRACTION16chain 'C' and (resid 545 through 631 )
17X-RAY DIFFRACTION17chain 'C' and (resid 632 through 687 )
18X-RAY DIFFRACTION18chain 'C' and (resid 688 through 878 )
19X-RAY DIFFRACTION19chain 'C' and (resid 879 through 932 )
20X-RAY DIFFRACTION20chain 'C' and (resid 933 through 1043 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 591 )
22X-RAY DIFFRACTION22chain 'D' and (resid 592 through 880 )
23X-RAY DIFFRACTION23chain 'D' and (resid 881 through 1042 )
24X-RAY DIFFRACTION24chain 'E' and (resid 2 through 428 )
25X-RAY DIFFRACTION25chain 'E' and (resid 429 through 665 )
26X-RAY DIFFRACTION26chain 'E' and (resid 666 through 804 )
27X-RAY DIFFRACTION27chain 'E' and (resid 805 through 904 )
28X-RAY DIFFRACTION28chain 'E' and (resid 905 through 1043 )
29X-RAY DIFFRACTION29chain 'F' and (resid 1 through 331 )
30X-RAY DIFFRACTION30chain 'F' and (resid 332 through 544 )
31X-RAY DIFFRACTION31chain 'F' and (resid 545 through 716 )
32X-RAY DIFFRACTION32chain 'F' and (resid 717 through 963 )
33X-RAY DIFFRACTION33chain 'F' and (resid 964 through 1043 )

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