[English] 日本語
Yorodumi
- PDB-29px: Crystal structure of the staphylococcal efflux pump QacA in the o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29px
TitleCrystal structure of the staphylococcal efflux pump QacA in the outward open state bound to ethidium
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 / Ethidium Bromide
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
ETHIDIUM / OXAMIC ACID / L(+)-TARTARIC ACID / Antiseptic resistance protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 27, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antiseptic resistance protein
B: Antiseptic resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,81116
Polymers111,5692
Non-polymers3,24214
Water00
1
A: Antiseptic resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1639
Polymers55,7841
Non-polymers1,3798
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antiseptic resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6477
Polymers55,7841
Non-polymers1,8636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.281, 169.861, 61.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Sugars , 2 types, 6 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
#6: 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

-
Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-OXM / OXAMIC ACID


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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.44 %
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)

-
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: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.789→110.843 Å / Num. obs: 14427 / % possible obs: 91.1 % / Redundancy: 26.3 % / Biso Wilson estimate: 101.95 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.022 / Net I/σ(I): 14.4
Reflection shellResolution: 2.789→3.214 Å / Num. unique obs: 722 / CC1/2: 0.808 / Rpim(I) all: 0.453

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→110.84 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.82 / SU B: 64.887 / SU ML: 0.582 / Cross valid method: THROUGHOUT / ESU R Free: 1.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.35111 746 5.2 %RANDOM
Rwork0.32148 ---
obs0.32312 13681 36.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--0.39 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.79→110.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 204 0 7499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127645
X-RAY DIFFRACTIONr_bond_other_d00.0167470
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.75310429
X-RAY DIFFRACTIONr_angle_other_deg0.51.6717219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.96851006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.555515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52101152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.21337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028488
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021556
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_it034033
X-RAY DIFFRACTIONr_mcbond_other034034
X-RAY DIFFRACTIONr_mcangle_it05.415036
X-RAY DIFFRACTIONr_mcangle_other05.415037
X-RAY DIFFRACTIONr_scbond_it03.0163612
X-RAY DIFFRACTIONr_scbond_other03.0163613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other05.65394
X-RAY DIFFRACTIONr_long_range_B_refined0.07927.988789
X-RAY DIFFRACTIONr_long_range_B_other0.07927.988790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.861 Å
RfactorNum. reflection% reflection
Rfree0.19 1 -
Rwork0.405 46 -
obs--1.66 %
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)
10.8294-0.33590.20440.76740.19570.4706-0.0882-0.03150.11350.17950.05660.0436-0.07810.09990.03160.0908-0.02150.02280.04970.00660.043338.006118.077717.9864
21.36520.009-0.05850.7166-0.00280.54190.0013-0.0862-0.3355-0.04990.0008-0.01730.30060.0222-0.00210.17090.0101-0.00840.00610.02060.083237.6949-22.559511.9817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 607
2X-RAY DIFFRACTION2B10 - 604

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more