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- PDB-6zod: Fusidic acid binding to the allosteric deep transmembrane domain ... -

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Basic information

Entry
Database: PDB / ID: 6zod
TitleFusidic acid binding to the allosteric deep transmembrane domain binding pocket, TM7/TM8 groove, and TM1/TM2 groove of the fully induced AcrB T 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 / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / 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
Octadecane / DECANE / DODECANE / FUSIDIC ACID / HEXANE / TRIETHYLENE GLYCOL / PHOSPHATIDYLETHANOLAMINE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsOswald, C. / Tam, H.K. / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)390,49446
Polymers380,8445
Non-polymers9,65041
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40860 Å2
ΔGint-114 kcal/mol
Surface area124380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.985, 166.129, 243.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 114736.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (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 / Cell line (production host): XL1 BLUE / Production host: Escherichia coli K-12 (bacteria)

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Sugars , 1 types, 7 molecules

#3: 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

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Non-polymers , 11 types, 183 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#7: Chemical
ChemComp-FUA / FUSIDIC ACID


Mass: 516.709 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H48O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, Antimicrobial*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


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


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#13: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.74 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.05M ADA, PH 6.9, 0.15-0.25M AMMONIUM REMARK 280 SULFATE, 5% GLYCEROL, 5-10% PEG4000, 0.001 M FUSIDIC ACID, 0.001M OXACILLIN, 0.001M ERYTHROMYCIN, 0.001M LINEZOLID

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→49.12 Å / Num. obs: 134919 / % possible obs: 97.7 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.069 / Rrim(I) all: 0.157 / Net I/σ(I): 8.1 / Num. measured all: 635542 / Scaling rejects: 584
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-2.94.61.7781.267480.5180.8771.99199.2
15.61-49.124.50.0428590.9970.0250.04990.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PHENIX3707refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 2.85→49.12 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 6706 4.98 %
Rwork0.2048 128056 -
obs0.2069 128056 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.79 Å2 / Biso mean: 78.3286 Å2 / Biso min: 25.76 Å2
Refinement stepCycle: final / Resolution: 2.85→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25775 0 782 149 26706
Biso mean--118.32 60.53 -
Num. residues----3391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.880.36642260.32144291451799
2.88-2.920.34852330.30484308454199
2.92-2.950.37032290.30854266449599
2.95-2.990.34432300.29994277450798
2.99-3.030.33192110.28144257446898
3.03-3.070.31782280.25994251447998
3.07-3.110.30082130.25244307452099
3.11-3.160.31982190.25314276449599
3.16-3.210.31162190.24384250446998
3.21-3.260.28112140.2354354456899
3.26-3.320.29572320.24854284451699
3.32-3.380.29262030.24964272447599
3.38-3.440.33182050.24524300450598
3.44-3.510.3062440.23424264450898
3.51-3.590.26642320.20994263449598
3.59-3.670.25542130.19844285449898
3.67-3.770.2552440.19324197444197
3.77-3.870.23542380.1894253449197
3.87-3.980.22562340.18664235446998
3.98-4.110.22122120.18794301451398
4.11-4.260.23282370.17874243448097
4.26-4.430.18212240.16814286451097
4.43-4.630.23822020.16654254445697
4.63-4.870.18432120.16294263447597
4.87-5.180.21412300.17394200443095
5.18-5.580.2532460.19484236448296
5.58-6.140.24662220.2084252447496
6.14-7.020.24392260.20754240446695
7.02-8.840.19412280.16374237446594
8.84-49.120.23392000.21974354455492
Refinement TLS params.Method: refined / Origin x: 40.165 Å / Origin y: -31.5236 Å / Origin z: -31.2966 Å
111213212223313233
T0.3567 Å20.0403 Å2-0.008 Å2-0.3467 Å20.0278 Å2--0.3321 Å2
L0.4411 °20.053 °20.0045 °2-0.2635 °2-0.084 °2--0.3143 °2
S0.0695 Å °0.1451 Å °0.0455 Å °-0.052 Å °-0.0616 Å °0.0193 Å °0.0063 Å °0.0124 Å °-0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1033
2X-RAY DIFFRACTION1allA1101 - 3401
3X-RAY DIFFRACTION1allB1 - 2701
4X-RAY DIFFRACTION1allC1 - 2901
5X-RAY DIFFRACTION1allD13 - 166
6X-RAY DIFFRACTION1allD201 - 301
7X-RAY DIFFRACTION1allE14 - 165
8X-RAY DIFFRACTION1allG2 - 200
9X-RAY DIFFRACTION1allH1 - 6
10X-RAY DIFFRACTION1allJ1 - 4
11X-RAY DIFFRACTION1allF1
12X-RAY DIFFRACTION1allI1

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