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- PDB-29on: Crystal structure of the staphylococcal efflux pump QacA in the i... -

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Basic information

Entry
Database: PDB / ID: 29on
TitleCrystal structure of the staphylococcal efflux pump QacA in the inward open state in complex with nanobody 89
Components
  • Antiseptic resistance protein
  • Nanobody 89
KeywordsMEMBRANE PROTEIN / Multidrug efflux pump / Major Facilitator Superfamily / MFS / DHA2 family / Antimicrobial resistance / Drug resistance / Proton-coupled transport / Drug-proton antiport / 14-transmembrane helix / Secondary active transporter / Cationic substrate efflux / Nanobody / Single-domain Indian camelid antibody
Function / homology
Function and homology information


transmembrane transporter activity / response to antibiotic / plasma membrane
Similarity search - Function
Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
OXAMIC ACID / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / Antiseptic resistance protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsJodaitis, L. / Hutchin, A. / Govaerts, C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS) Belgium
CitationJournal: To Be Published
Title: Structural and dynamic insights into the staphylococcal efflux pump QacA reveal multidrug transport mechanisms and substrate specificity determinants
Authors: Jodaitis, L. / Sutton, P. / Hutchin, A. / Dashtbani-Roozbehani, A. / Martens, C. / Coppieters, K. / Pardon, E. / Steyaert, J. / O'Mara, M. / Brown, M. / Govaerts, C.
History
DepositionMar 26, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 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: Antiseptic resistance protein
B: Antiseptic resistance protein
C: Nanobody 89
D: Nanobody 89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,86712
Polymers143,5004
Non-polymers4,3688
Water00
1
A: Antiseptic resistance protein
C: Nanobody 89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2778
Polymers71,7502
Non-polymers3,5286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antiseptic resistance protein
D: Nanobody 89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5904
Polymers71,7502
Non-polymers8402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.304, 94.335, 98.306
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody / Sugars , 3 types, 8 molecules ABCD

#1: Protein Antiseptic resistance protein / Quaternary ammonium compound efflux MFS transporter


Mass: 55784.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: qacA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0J9
#2: Antibody Nanobody 89


Mass: 15965.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 4 molecules

#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#6: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3

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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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer ...Details: 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer system 1 (Imidazole; MES monohydrate) pH 6.5 and 50% precipitant mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.32→93.354 Å / Num. obs: 17025 / % possible obs: 90.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 71.85 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.134 / Rrim(I) all: 0.356 / Net I/σ(I): 4.9
Reflection shellResolution: 3.32→3.787 Å / Num. unique obs: 851 / CC1/2: 0.625

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-JUL-2025)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→31.53 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.833 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3265 838 4.93 %RANDOM
Rwork0.2972 ---
obs0.2986 16161 66.84 %-
Displacement parametersBiso mean: 82.77 Å2
Baniso -1Baniso -2Baniso -3
1--8.9597 Å20 Å20.9618 Å2
2--6.611 Å20 Å2
3---2.3486 Å2
Refine analyzeLuzzati coordinate error obs: 0.682 Å
Refinement stepCycle: LAST / Resolution: 3.32→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9079 0 0 0 9079
LS refinement shellResolution: 3.32→3.6 Å / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.3868 -6.51 %
Rwork0.3373 388 -
all0.3405 415 -
obs--7.67 %

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