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- PDB-6zog: Minocycline binding to the deep binding pocket of AcrB-I38F_I671T -

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Basic information

Entry
Database: PDB / ID: 6zog
TitleMinocycline binding to the deep binding pocket of AcrB-I38F_I671T
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
Octadecane / TETRADECANE / DECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / (2S)-3-hydroxypropane-1,2-diyl didecanoate / Chem-MIY / PENTADECANE / 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: 2.75 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
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)388,12336
Polymers380,9105
Non-polymers7,21331
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37960 Å2
ΔGint-100 kcal/mol
Surface area122860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.965, 161.954, 245.288
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: 114758.258 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 / Comment: detergent*YM

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Non-polymers , 14 types, 158 molecules

#4: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DDR / (2S)-3-hydroxypropane-1,2-diyl didecanoate / 1,2-DIDECANOYL-SN-GLYCEROL


Mass: 400.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O5
#7: Chemical ChemComp-MYS / PENTADECANE / Pentadecane


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#8: Chemical ChemComp-8K6 / Octadecane / N-Octadecane / Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#9: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE / Minocycline


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#12: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#13: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#14: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#15: Chemical ChemComp-C14 / TETRADECANE / Tetradecane


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#16: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.67 Å3/Da / Density % sol: 66.53 %
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, 0.002M MINOCYCLINE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.75→49.59 Å / Num. obs: 151127 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.074 / Rrim(I) all: 0.205 / Net I/σ(I): 9.8 / Num. measured all: 1141557 / Scaling rejects: 256
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.87.72.0681.274130.4960.7972.219100
15.06-49.596.50.04110270.9890.0230.04897.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 2.75→49.59 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.882 / SU B: 18.141 / SU ML: 0.321 / SU R Cruickshank DPI: 0.5452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 7492 5 %RANDOM
Rwork0.2303 ---
obs0.2322 143539 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.54 Å2 / Biso mean: 61.673 Å2 / Biso min: 26 Å2
Baniso -1Baniso -2Baniso -3
1--4.68 Å2-0 Å20 Å2
2--6.93 Å2-0 Å2
3----2.25 Å2
Refinement stepCycle: final / Resolution: 2.75→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25924 0 491 133 26548
Biso mean--93.81 39.98 -
Num. residues----3413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01326949
X-RAY DIFFRACTIONr_bond_other_d0.0010.01725937
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.64436528
X-RAY DIFFRACTIONr_angle_other_deg1.031.57960080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.66953420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00923.1451183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16154438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.87915120
X-RAY DIFFRACTIONr_chiral_restr0.0320.23625
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0229728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025344
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 536 -
Rwork0.377 10481 -
all-11017 -
obs--100 %

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