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- PDB-6z70: Structure of the MATE family multidrug resistance transporter Aq_... -

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Basic information

Entry
Database: PDB / ID: 6z70
TitleStructure of the MATE family multidrug resistance transporter Aq_128 from Aquifex aeolicus in the outward-facing state
ComponentsAq128
KeywordsMEMBRANE PROTEIN / MATE class transporter
Function / homology
Function and homology information


antiporter activity / xenobiotic transmembrane transporter activity / monoatomic ion transport / plasma membrane
Similarity search - Function
: / : / Multi antimicrobial extrusion protein / MatE
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Multidrug-efflux transporter
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhao, J. / Safarian, S. / Thielmann, Y. / Xie, H. / Wang, J. / Michel, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily.
Authors: Zhao, J. / Xie, H. / Mehdipour, A.R. / Safarian, S. / Ermler, U. / Munke, C. / Thielmann, Y. / Hummer, G. / Ebersberger, I. / Wang, J. / Michel, H.
History
DepositionMay 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aq128
B: Aq128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6309
Polymers111,1342
Non-polymers2,4967
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Dimer in solution confirmed by BN_PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-36 kcal/mol
Surface area34360 Å2
Unit cell
Length a, b, c (Å)72.100, 116.100, 137.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 1 through 236 or (resid 237...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUchain AAA1 - 4441 - 444
21METMETLEULEU(chain B and (resid 1 through 236 or (resid 237...BB1 - 2361 - 236
22PHEPHEPHEPHE(chain B and (resid 1 through 236 or (resid 237...BB237237
23METMETLEULEU(chain B and (resid 1 through 236 or (resid 237...BB1 - 4441 - 444

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Components

#1: Protein Aq128


Mass: 55567.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Gene: aq_128 / Cell line (production host): Top10 / Production host: Escherichia coli (E. coli) / References: UniProt: O66528
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 5
Details: 0.1 M Sodium Citrate-Citric acid 30% PEG 500 DME (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.76 Å / Num. obs: 78497 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6 % / Rmerge(I) obs: 1.113 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7755 / CC1/2: 0.855 / Rpim(I) all: 0.489 / Rrim(I) all: 1.217 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FV6

6fv6


Resolution: 2→19.986 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 36.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1427 5 %
Rwork0.2657 147576 -
obs0.2659 78497 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.87 Å2 / Biso mean: 41.4618 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 2→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6973 0 175 6 7154
Biso mean--53.49 41.71 -
Num. residues----888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2676X-RAY DIFFRACTION6.856TORSIONAL
12B2676X-RAY DIFFRACTION6.856TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.07140.3711600.3571481799
2.0714-2.15430.3311240.32631481599
2.1543-2.25220.34881580.30081484099
2.2522-2.37070.28491580.28331471499
2.3707-2.5190.27441100.26871479899
2.519-2.71310.34291350.26381481999
2.7131-2.98530.33711680.26891482599
2.9853-3.41540.26611590.27051476999
3.4154-4.2960.3111230.24751475299
4.296-19.9860.21021320.24721442797

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