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- PDB-9hci: structure of the double Cys-substituted cross-linked AcrB variant... -

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Basic information

Entry
Database: PDB / ID: 9hci
Titlestructure of the double Cys-substituted cross-linked AcrB variant S562C_T837C
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / RND multidrug efflux pump / antimicrobial resistance / intermediate conformational state / crosslinked structure
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
TETRADECANE / DECANE / DODECANE / nonane / HEXANE / N-OCTANE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrandstaetter, L. / Mueller, R.T. / Pos, K.M.
Funding support Switzerland, Germany, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
University of Zurich Switzerland
German Research Foundation (DFG)SFB 807 Germany
CitationJournal: To Be Published
Title: Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps
Authors: Boernsen, C. / Mueller, R.T. / Pos, K.M.
History
DepositionNov 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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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)389,32850
Polymers380,8985
Non-polymers8,43045
Water21,8881215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42140 Å2
ΔGint-21 kcal/mol
Surface area120790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.710, 165.300, 244.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 114754.398 Da / Num. of mol.: 3 / Mutation: S562C, T837C
Source method: isolated from a genetically manipulated source
Details: disulfide bond between S562C and T837C / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MG1655 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24a / Details (production host): pET24a_acrB_S562C_T837C / Production host: Escherichia coli B (bacteria) / Strain (production host): C43(DE3)DELTAacrB / 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) / Plasmid: pQE30 / Details (production host): pQE30_110819 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): XL1-Blue

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Sugars , 1 types, 8 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 1252 molecules

#4: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / 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-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#9: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#10: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#11: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.87 Å3/Da / Density % sol: 68.23 % / Description: Rod-shaped crystals
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ADA, pH 6.5, 0.2M ammonium sulfate, 8% PEG4000, 5.1% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2007
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.6→47.69 Å / Num. obs: 181397 / % possible obs: 99.94 % / Redundancy: 8.4 % / CC1/2: 0.982 / Net I/σ(I): 7.09
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 17959 / CC1/2: 0.683 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PDB-REDO8.11refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.69 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.063 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 9291 5.1 %RANDOM
Rwork0.18974 ---
obs0.19177 172106 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.783 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å2-0 Å2
2--0.05 Å2-0 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25975 0 576 1215 27766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01727022
X-RAY DIFFRACTIONr_bond_other_d0.0010.01626696
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.8236576
X-RAY DIFFRACTIONr_angle_other_deg0.4611.57761412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275.173535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.029104447
X-RAY DIFFRACTIONr_chiral_restr0.0610.24320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0230828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025896
X-RAY DIFFRACTIONr_mcbond_it4.4231.45613672
X-RAY DIFFRACTIONr_mcbond_other4.4211.45613672
X-RAY DIFFRACTIONr_mcangle_it6.2932.61117083
X-RAY DIFFRACTIONr_mcangle_other6.2932.61217084
X-RAY DIFFRACTIONr_scbond_it7.6212.13513350
X-RAY DIFFRACTIONr_scbond_other7.6262.13613351
X-RAY DIFFRACTIONr_scangle_other9.9673.61519494
X-RAY DIFFRACTIONr_long_range_B_refined11.44115.0730335
X-RAY DIFFRACTIONr_long_range_B_other11.45514.8830033
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 652 -
Rwork0.338 12595 -
obs--99.98 %
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)
10.6676-0.0388-0.10850.3611-0.23980.85340.1340.00060.31860.0813-0.0375-0.015-0.39540.0251-0.09650.1961-0.02560.08450.39740.00170.154829.387-15.288-16.494
20.3101-0.10070.05880.5521-0.39050.44640.08240.2758-0.006-0.2953-0.02710.13660.1796-0.0727-0.05530.19120.0363-0.08690.53640.00060.048429.191-41.57-52.379
30.57850.0241-0.07270.1513-0.0940.61080.06320.18110.1085-0.0653-0.072-0.0386-0.05190.13650.00890.05190.01880.03120.46090.06780.033167.671-26.444-34.003
42.36180.22151.30511.33660.14994.11240.0042-0.0306-0.1021-0.0123-0.06290.2638-0.0315-0.40910.05870.1154-0.1128-0.0480.3139-0.09990.18191.075-75.406-24.619
54.2351-1.6556-0.85464.24980.8592.6583-0.075-0.77330.62050.48560.1171-0.4929-0.35360.1738-0.04210.187-0.1444-0.07210.73-0.08880.115946.585-39.41927.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1044
2X-RAY DIFFRACTION2B1 - 1033
3X-RAY DIFFRACTION3C1 - 1033
4X-RAY DIFFRACTION4D12 - 166
5X-RAY DIFFRACTION5E14 - 166

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