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- PDB-6zoh: 3-Formylrifamycin SV binding to the access pocket of AcrB-G619P_G... -

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Basic information

Entry
Database: PDB / ID: 6zoh
Title3-Formylrifamycin SV binding to the access pocket of AcrB-G619P_G621P L and T protomers
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
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Chem-3YI / DECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / (2S)-3-hydroxypropane-1,2-diyl didecanoate / HEXANE / Chem-LPX / 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: 2.8 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)390,08640
Polymers381,0845
Non-polymers9,00235
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38100 Å2
ΔGint-19 kcal/mol
Surface area120300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.143, 160.129, 243.588
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: 114816.414 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, 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, 266 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#8: 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.: 2 / Source method: obtained synthetically / Formula: C38H47NO13 / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#11: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#12: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO7P
#13: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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 QUINONE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→49.19 Å / Num. obs: 139909 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.09 / Rrim(I) all: 0.227 / Net I/σ(I): 7.6 / Num. measured all: 877116 / Scaling rejects: 1603
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.856.32.11168870.3730.9072.3100
15.34-49.195.40.0539420.9920.0280.0697.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5jmn


Resolution: 2.8→49.19 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.879 / SU ML: 0.283 / SU R Cruickshank DPI: 0.6466 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.647 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 6765 4.8 %RANDOM
Rwork0.223 ---
obs0.2241 133053 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.25 Å2 / Biso mean: 59.655 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å20 Å2-0 Å2
2--3.76 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 2.8→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25903 0 619 244 26766
Biso mean--94.02 40.13 -
Num. residues----3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01327034
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726104
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.6536640
X-RAY DIFFRACTIONr_angle_other_deg1.0381.58560470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14453409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86823.1771174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.293154434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.34615120
X-RAY DIFFRACTIONr_chiral_restr0.0330.23652
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0229667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025317
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 456 -
Rwork0.355 9717 -
all-10173 -
obs--100 %

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