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- PDB-21fo: CYMAL-7-bound MexB -

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Basic information

Entry
Database: PDB / ID: 21fo
TitleCYMAL-7-bound MexB
ComponentsMultidrug resistance protein MexB
KeywordsMEMBRANE PROTEIN / Drug efflux / RND transporter
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
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-CA7 / Multidrug resistance protein MexB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUeda, Y. / Yonehara, R. / Nakagawa, A. / Yamashita, E.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03167 Japan
Japan Society for the Promotion of Science (JSPS)25291014 Japan
CitationJournal: J.Biochem. / Year: 2026
Title: Structure of chloramphenicol-bound MexB reveals residues in the distal binding pocket that are critical for substrate recognition.
Authors: Ueda, Y. / Yonehara, R. / Ishizaka-Ikeda, E. / Nakagawa, A. / Yamashita, E.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: 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 resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,8905
Polymers341,8453
Non-polymers1,0452
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18820 Å2
ΔGint-78 kcal/mol
Surface area109330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.041, 168.871, 172.210
Angle α, β, γ (deg.)90.000, 102.226, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 113948.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexB, PA0426 / Production host: Escherichia coli (E. coli) / References: UniProt: P52002
#2: Chemical ChemComp-CA7 / 7-cyclohexylheptyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 522.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H46O11 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH8.0, 0.2 M KCl, 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→40.55 Å / Num. obs: 251734 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 55.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.1
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 7726 / CC1/2: 0.406

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.55 Å / SU ML: 0.3264 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 12407 4.93 %
Rwork0.2205 239327 -
obs0.2222 251734 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23388 0 72 0 23460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008423939
X-RAY DIFFRACTIONf_angle_d0.96432533
X-RAY DIFFRACTIONf_chiral_restr0.05463808
X-RAY DIFFRACTIONf_plane_restr0.00824163
X-RAY DIFFRACTIONf_dihedral_angle_d17.0828749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.37643980.34437328X-RAY DIFFRACTION91.22
2.33-2.350.35653720.33597972X-RAY DIFFRACTION98.28
2.35-2.380.36764010.33048014X-RAY DIFFRACTION98.4
2.38-2.410.33433930.31887907X-RAY DIFFRACTION98.48
2.41-2.440.33624320.30728000X-RAY DIFFRACTION98.48
2.44-2.480.36054420.30157906X-RAY DIFFRACTION98.62
2.48-2.510.32474300.29637980X-RAY DIFFRACTION98.59
2.51-2.550.3384310.28347932X-RAY DIFFRACTION98.68
2.55-2.590.33214250.28127972X-RAY DIFFRACTION98.82
2.59-2.630.3044170.26658013X-RAY DIFFRACTION98.85
2.63-2.680.29754270.27098019X-RAY DIFFRACTION98.93
2.68-2.730.32254100.26018059X-RAY DIFFRACTION98.95
2.73-2.780.29734120.25878002X-RAY DIFFRACTION99.05
2.78-2.840.28714570.2567921X-RAY DIFFRACTION98.93
2.84-2.90.31213940.2538080X-RAY DIFFRACTION99.01
2.9-2.960.27034270.23458034X-RAY DIFFRACTION99.1
2.96-3.040.27464020.23718026X-RAY DIFFRACTION99.2
3.04-3.120.29813960.25428061X-RAY DIFFRACTION99.28
3.12-3.210.30083710.25558090X-RAY DIFFRACTION99.33
3.21-3.320.27394030.24858067X-RAY DIFFRACTION99.35
3.32-3.430.27533940.23878069X-RAY DIFFRACTION99.44
3.43-3.570.27614310.23068070X-RAY DIFFRACTION99.51
3.57-3.730.25733930.21928104X-RAY DIFFRACTION99.47
3.73-3.930.23334220.20638080X-RAY DIFFRACTION99.44
3.93-4.180.24274150.20118088X-RAY DIFFRACTION99.35
4.18-4.50.21514270.19248066X-RAY DIFFRACTION99.61
4.5-4.950.21764430.18378106X-RAY DIFFRACTION99.52
4.95-5.670.23854320.2028074X-RAY DIFFRACTION99.5
5.67-7.130.23634260.20278171X-RAY DIFFRACTION99.62
7.13-40.550.1993840.16597116X-RAY DIFFRACTION86.21
Refinement TLS params.Method: refined / Origin x: 45.185785263 Å / Origin y: 0.43957607791 Å / Origin z: 26.8466667803 Å
111213212223313233
T0.460112672074 Å2-0.0464338191377 Å20.0167413455787 Å2-0.409643850925 Å20.0234923411733 Å2--0.428543354689 Å2
L0.788451294366 °2-0.0484885541428 °20.215505295386 °2-0.740941995546 °2-0.178401407242 °2--1.22441656379 °2
S0.019590876039 Å °-0.141768479757 Å °-0.0294599330673 Å °0.174030316228 Å °-0.0499519729834 Å °-0.209064014185 Å °-0.0552088105596 Å °0.355248755613 Å °0.0234497665077 Å °
Refinement TLS groupSelection details: all

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