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- PDB-29om: Crystal structure of the staphylococcal efflux pump QacA in the o... -

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Basic information

Entry
Database: PDB / ID: 29om
TitleCrystal structure of the staphylococcal efflux pump QacA in the outward open state
ComponentsAntiseptic resistance protein
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
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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / Antiseptic resistance protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.831 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,04027
Polymers111,5692
Non-polymers11,47225
Water1,22568
1
A: Antiseptic resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,26418
Polymers55,7841
Non-polymers9,48017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antiseptic resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7779
Polymers55,7841
Non-polymers1,9928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.703, 74.214, 279.059
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 / Sugars , 2 types, 12 molecules AB

#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
#3: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 83 molecules

#2: 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
#4: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H77O8P
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 58.03 %
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: 2.822→69.766 Å / Num. obs: 26962 / % possible obs: 92.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 98.55 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.4
Reflection shellResolution: 2.822→3.028 Å / Num. unique obs: 1348 / CC1/2: 0.552

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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: 2.831→46.51 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.51
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1240 4.61 %RANDOM
Rwork0.3102 ---
obs0.311 26900 85.4 %-
Displacement parametersBiso mean: 88.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.6497 Å20 Å20 Å2
2---4.0982 Å20 Å2
3---5.7479 Å2
Refine analyzeLuzzati coordinate error obs: 0.595 Å
Refinement stepCycle: LAST / Resolution: 2.831→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7570 0 0 71 7641
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0068404HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8611343HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3076SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1256HARMONIC5
X-RAY DIFFRACTIONt_it8404HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion19.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1187SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7009SEMIHARMONIC4
LS refinement shellResolution: 2.831→2.98 Å
RfactorNum. reflection% reflection
Rfree0.4608 -3.53 %
Rwork0.3049 519 -
obs--12.56 %

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