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- PDB-6zoc: Erythromycin binding to the access pocket of AcrB-G616P L protome... -

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Basic information

Entry
Database: PDB / ID: 6zoc
TitleErythromycin binding to the access pocket of AcrB-G616P L protomer and 3-formylrifamycin SV binding to the access pocket of AcrB-G616P T protomer
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug efflux pump / Membrane protein
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport ...alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3YI / TETRADECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / ERYTHROMYCIN A / HEXANE / 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: 2.89 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)388,64242
Polymers380,9645
Non-polymers7,67837
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39490 Å2
ΔGint-80 kcal/mol
Surface area119190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.327, 161.26, 244.023
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: 114776.352 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, 5 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 221 molecules

#3: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#9: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#10: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#11: Chemical ChemComp-3YI / (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate / 3-formyl rifamycin SV


Mass: 725.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H47NO13 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#13: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#14: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#15: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.59 Å3/Da / Density % sol: 65.71 %
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, 0.003M RIFAMPICIN, 0.001M ERYTHROMYCIN, 0.001M FUSIDIC ACID, 0.001M LINEZOLID, 0.001M OXACILLIN

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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: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→49.43 Å / Num. obs: 129623 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 48.59 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.604 / Rpim(I) all: 0.21 / Rrim(I) all: 0.64 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.89-2.9496.3740.563320.4062.2256.757100
15.81-49.437.90.0648900.9990.0250.06997.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 2.89→49.37 Å / Cor.coef. Fo:Fc: 0.843 / Cor.coef. Fo:Fc free: 0.828 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.414
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 4399 -RANDOM
Rwork0.2184 ---
obs0.2193 88443 67.7 %-
Displacement parametersBiso mean: 38.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.2434 Å20 Å20 Å2
2--4.9007 Å20 Å2
3----0.6573 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.89→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25903 0 523 189 26615
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00527174HARMONIC1.8
X-RAY DIFFRACTIONt_angle_deg0.5437069HARMONIC3.1
X-RAY DIFFRACTIONt_dihedral_angle_d9409SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4484HARMONIC5
X-RAY DIFFRACTIONt_it26897HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3632SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact20691SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion16.86
LS refinement shellResolution: 2.89→3.08 Å
RfactorNum. reflection% reflection
Rfree0.2891 77 -
Rwork0.2662 --
obs0.2672 1769 7.3 %
Refinement TLS params.

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)
10.28840.0946-0.13520.2967-0.11790.31650.12240.0222-0.08030.0222-0.0311-0.0827-0.0803-0.0827-0.0913-0.06460.03080.06090.0506-0.0342-0.015429.5656-15.2608-15.9119
20.2794-0.0018-0.02220.265-0.150.14480.0588-0.07180.0949-0.0718-0.0228-0.06740.0949-0.0674-0.0361-0.06860.0308-0.07670.1701-0.0293-0.062128.9136-41.0574-51.9984
30.38840.0348-0.12040.1419-0.24420.5050.0509-0.0491-0.0033-0.0491-0.02260.0765-0.00330.0765-0.0283-0.0824-0.0114-0.00030.05180.0216-0.031267.3545-26.2197-34.4951
43.2475-0.06622.46710.7023-0.9477.7056-0.09090.14330.02010.1433-0.1685-0.33010.0201-0.33010.2594-0.1372-0.16310.0276-0.0382-0.1142-0.0171.0707-73.9904-23.9922
53.7055-2.2791-0.47695.9796-0.06912.01040.05240.8837-0.26310.8837-0.05310.2176-0.26310.21760.0008-0.2142-0.1479-0.11970.3698-0.0527-0.374347.2762-39.449728.1946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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