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- PDB-3w9i: Structural basis for the inhibition of bacterial multidrug exporters -

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Basic information

Entry
Database: PDB / ID: 3w9i
TitleStructural basis for the inhibition of bacterial multidrug exporters
ComponentsMultidrug resistance protein MexB
KeywordsMEMBRANE PROTEIN / MexB / Efflux pump / Transporter / Multidrug efflux pump / MexA / OprM / Inner Membrane / Transport protein
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transport / response to antibiotic / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / 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 ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / 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 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Multidrug resistance protein MexB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsSakurai, K. / Nakashima, R. / Hayashi, K. / Yamaguchi, A.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the inhibition of bacterial multidrug exporters
Authors: Nakashima, R. / Sakurai, K. / Yamasaki, S. / Hayashi, K. / Nagata, C. / Hoshino, K. / Onodera, Y. / Nishino, K. / Yamaguchi, A.
History
DepositionApr 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
D: Multidrug resistance protein MexB
E: Multidrug resistance protein MexB
F: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)685,43322
Polymers677,2636
Non-polymers8,17016
Water1267
1
A: Multidrug resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,71611
Polymers338,6313
Non-polymers4,0858
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26790 Å2
ΔGint-98 kcal/mol
Surface area107160 Å2
MethodPISA
2
D: Multidrug resistance protein MexB
E: Multidrug resistance protein MexB
F: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,71611
Polymers338,6313
Non-polymers4,0858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26140 Å2
ΔGint-99 kcal/mol
Surface area108530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.815, 133.981, 150.467
Angle α, β, γ (deg.)87.14, 69.49, 88.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 1030 / Label seq-ID: 1 - 1030

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DD
12BB
22EE
13CC
23FF

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.612914, 0.665371, 0.426167), (0.665791, 0.144445, 0.732023), (0.425509, 0.732405, -0.53153)-9.6414, 7.20559, 11.39539

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Components

#1: Protein
Multidrug resistance protein MexB / Multidrug-efflux transporter MexB


Mass: 112877.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: mexB, PA0426 / Plasmid: pUCP20 / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P52002
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50mM Na Acetate-HCl pH5.0, 300mM NaCl, 25% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 23, 2011
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 241501 / % possible obs: 97.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.753.70.552196.9
2.75-2.83.70.445197.4
2.8-2.853.70.382197.7
2.85-2.913.80.329197.3
2.91-2.973.80.274197.8
2.97-3.043.80.224198.2
3.04-3.123.80.181198.2
3.12-3.23.80.15198.7
3.2-3.33.80.123198.8
3.3-3.43.90.094199
3.4-3.523.90.075199.1
3.52-3.663.90.064199.1
3.66-3.833.90.051199.2
3.83-4.033.80.044199.2
4.03-4.293.80.038199.2
4.29-4.623.80.034199.1
4.62-5.083.80.032198.9
5.08-5.823.90.032199.6
5.82-7.333.90.028199.6
7.33-1003.70.024177.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.35 Å48.33 Å
Translation3.35 Å48.33 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V50

2v50


Resolution: 2.71→48.33 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.3 / SU ML: 0.318 / SU R Cruickshank DPI: 0.8203 / Cross valid method: THROUGHOUT / ESU R: 0.862 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31529 12079 5 %RANDOM
Rwork0.28176 ---
obs0.28346 228777 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20.02 Å20.02 Å2
2--0.06 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46738 0 560 7 47305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01948342
X-RAY DIFFRACTIONr_bond_other_d0.0020.0247367
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.98165669
X-RAY DIFFRACTIONr_angle_other_deg1.1993108907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.87356151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.62424.3981860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.059157908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.66315228
X-RAY DIFFRACTIONr_chiral_restr0.3450.27749
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02154173
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210603
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A15395MEDIUM POSITIONAL0.540.5
1A15395MEDIUM THERMAL12.862
2B15608MEDIUM POSITIONAL0.50.5
2B15608MEDIUM THERMAL11.772
3C15607MEDIUM POSITIONAL0.530.5
3C15607MEDIUM THERMAL8.672
LS refinement shellResolution: 2.708→2.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 900 -
Rwork0.392 16271 -
obs--93.29 %

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