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- PDB-6zoa: Partially induced AcrB T protomer and DDM binding to the TM8/PC2 ... -

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Basic information

Entry
Database: PDB / ID: 6zoa
TitlePartially induced AcrB T protomer and DDM binding to the TM8/PC2 pathway of AcrB L2 protomer
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug efflux pump / Membrane protein
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / outer membrane-bounded periplasmic space / membrane / identical protein binding / plasma membrane
Similarity search - Function
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
TETRADECANE / DECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / HEXANE / PENTANE / N-OCTANE / PHOSPHATIDYLETHANOLAMINE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsTam, H.K. / Foong, W.E. / Pos, K.M.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG-EXC115 Germany
German-Israeli Foundation for Research and DevelopmentI-1202-248.9/2012 Germany
European Communitys Seventh Framework ProgrammeFP7/2007-2013European Union
CitationJournal: Nat Commun / Year: 2021
Title: Allosteric drug transport mechanism of multidrug transporter AcrB.
Authors: Tam, H.K. / Foong, W.E. / Oswald, C. / Herrmann, A. / Zeng, H. / Pos, K.M.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
D: DARPIN
E: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,91038
Polymers380,8445
Non-polymers8,06633
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.596, 162.993, 246.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 15 - 166 / Label seq-ID: 15 - 166

Dom-IDAuth asym-IDLabel asym-ID
1DD
2EE

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.479834, -0.507791, -0.715478), (0.452267, 0.555634, -0.697658), (0.751807, -0.658346, -0.036955)24.233351, -55.441151, -84.364372

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Components

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Protein , 2 types, 5 molecules ABCDE

#1: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114736.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P31224
#2: Protein DARPIN /


Mass: 18317.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: ARTIFICIAL GENE / Plasmid: PQE30 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1 BLUE

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Sugars , 1 types, 6 molecules

#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 12 types, 302 molecules

#4: Chemical
ChemComp-C14 / TETRADECANE / Tetradecane


Mass: 198.388 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical
ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H27NO
#6: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14
#7: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-LNK / PENTANE / Pentane


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#14: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.7 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.05M ADA, PH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.001M DICLOXACILLIN, 0.001M OXACILLIN, 0.001M PIPERACILLIN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→49.68 Å / Num. obs: 111779 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.966 / Rmerge(I) obs: 0.289 / Rpim(I) all: 0.133 / Rrim(I) all: 0.319 / Net I/σ(I): 5.8 / Num. measured all: 613744 / Scaling rejects: 693
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.05-3.15.32.249154490.3441.052.48899.9
16.71-49.684.70.0637460.9560.0390.07595.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.21data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 3.05→49.68 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.873 / SU B: 51.724 / SU ML: 0.419 / SU R Cruickshank DPI: 0.3834 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 5610 5 %RANDOM
Rwork0.2402 ---
obs0.2418 106083 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.49 Å2 / Biso mean: 58.86 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å20 Å2
2--0.84 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 3.05→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25934 0 554 275 26763
Biso mean--82.28 31.72 -
Num. residues----3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01326964
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726156
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.64836504
X-RAY DIFFRACTIONr_angle_other_deg1.0341.59160588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47753407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6923.1531183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.592154443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.34715122
X-RAY DIFFRACTIONr_chiral_restr0.0350.23626
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0229597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025321
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: D / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
895MEDIUM POSITIONAL0.190.5
1348LOOSE POSITIONAL0.425
895MEDIUM THERMAL0.432
1348LOOSE THERMAL0.4210
LS refinement shellResolution: 3.05→3.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 412 -
Rwork0.367 7710 -
all-8122 -
obs--99.88 %
Refinement TLS params.

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

IDL11 (°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)
10.45350.0272-0.0580.6328-0.3370.69090.0618-0.01220.2430.1586-0.0266-0.0047-0.3011-0.0533-0.03520.13480.03730.03390.7589-0.02150.131629.194-15.0151-16.9801
20.22240.0396-0.04070.498-0.24030.23410.03620.20520.0028-0.27310.02270.11550.1627-0.085-0.05890.17990.0079-0.05170.8337-0.01230.084529.1767-41.8982-52.7452
30.43130.0364-0.08850.1988-0.1730.59930.02610.06920.0751-0.0363-0.0191-0.0308-0.03820.0498-0.0070.01890.00920.01510.6630.00590.021467.949-26.287-34.7775
42.6656-0.31471.61162.0435-0.27314.3393-0.0602-0.0160.04650.1057-0.09190.2483-0.1765-0.17750.15210.0893-0.12810.02070.5661-0.07930.2131.2843-75.5867-24.1081
53.3498-1.6315-0.6335.59140.97952.6941-0.0316-0.28580.40130.2916-0.0441-0.4457-0.27150.16680.07570.1776-0.1137-0.05710.788-0.01040.07747.3653-39.261528.2548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1042
2X-RAY DIFFRACTION2B1 - 1101
3X-RAY DIFFRACTION3C1 - 1035
4X-RAY DIFFRACTION4D11 - 166
5X-RAY DIFFRACTION5E13 - 166

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