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- PDB-6fv6: Monomer structure of the MATE family multidrug resistance transpo... -

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Basic information

Entry
Database: PDB / ID: 6fv6
TitleMonomer structure 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 VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsZhao, J. / Safarian, S. / Thielmann, Y. / Xie, H. / Wang, J. / Michel, H.
Funding support Germany, China, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation Germany
Tianjin University China
CitationJournal: To Be Published
Title: Monomer structure of Aq128 in the outward-facing state
Authors: Zhao, J. / Safarian, S. / Thielmann, Y. / Xie, H. / Wang, J. / Michel, H.
History
DepositionMar 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aq128


Theoretical massNumber of molelcules
Total (without water)52,6171
Polymers52,6171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Present as a dimer in solution but crystallizes as a monomer in vapor diffusion experiments.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.801, 149.801, 63.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aq128


Mass: 52617.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: aq_128 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / 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: 3.39 Å3/Da / Density % sol: 63.72 % / Description: plate
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M Tris 1.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→20 Å / Num. obs: 7452 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.057 / Rrim(I) all: 0.156 / Net I/σ(I): 9.6
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 8 % / Rmerge(I) obs: 1.778 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 739 / CC1/2: 0.616 / Rpim(I) all: 0.664 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mlb

4mlb


Resolution: 3.8→19.972 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.63
RfactorNum. reflection% reflection
Rfree0.326 691 5.14 %
Rwork0.2984 --
obs0.2996 7436 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→19.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 0 0 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033277
X-RAY DIFFRACTIONf_angle_d0.5924449
X-RAY DIFFRACTIONf_dihedral_angle_d10.8281884
X-RAY DIFFRACTIONf_chiral_restr0.039528
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.09110.36851400.38542541X-RAY DIFFRACTION99
4.0911-4.49850.43561330.35012575X-RAY DIFFRACTION100
4.4985-5.13980.37531370.33822556X-RAY DIFFRACTION100
5.1398-6.43930.37471380.35542542X-RAY DIFFRACTION100
6.4393-19.97260.25331430.23382542X-RAY DIFFRACTION99

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