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- PDB-6z71: Structure of the MATE family multidrug resistance transporter Aq_... -

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Basic information

Entry
Database: PDB / ID: 6z71
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: / : / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / monoatomic ion transport / plasma membrane / Multidrug-efflux transporter
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aq128
B: Aq128


Theoretical massNumber of molelcules
Total (without water)111,1342
Polymers111,1342
Non-polymers00
Water00
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 area1530 Å2
ΔGint-19 kcal/mol
Surface area38410 Å2
Unit cell
Length a, b, c (Å)80.300, 71.500, 104.300
Angle α, β, γ (deg.)90.000, 100.900, 90.000
Int Tables number4
Space group name H-MP1211

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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

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6
Details: 0.1 M MES 0.1 M Magnesium chloride 0.1 M Sodium chloride 30% PEG 600 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.81517 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81517 Å / Relative weight: 1
ReflectionResolution: 3.5→19.978 Å / Num. obs: 14759 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.11 / Rrim(I) all: 0.21 / Net I/σ(I): 6.4
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1453 / CC1/2: 0.618 / Rpim(I) all: 0.516 / Rrim(I) all: 0.989 / % possible all: 100

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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: 3.5→19.978 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3419 737 5 %
Rwork0.3124 14010 -
obs0.3138 14747 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.47 Å2 / Biso mean: 75.9581 Å2 / Biso min: 15.49 Å2
Refinement stepCycle: final / Resolution: 3.5→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 0 0 6632
Num. residues----842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.76860.3711460.366127812927100
3.7686-4.14480.36481470.335327682915100
4.1448-4.73750.36151450.305228012946100
4.7375-5.94260.30911480.324428122960100
5.9426-19.97780.32481510.27532848299999

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