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- PDB-6fv8: Dimer structure of the MATE family multidrug resistance transport... -

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Basic information

Entry
Database: PDB / ID: 6fv8
TitleDimer 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhao, J. / Safarian, S. / Thielmann, Y. / Xie, H. / Wang, J. / Michel, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation Germany
CitationJournal: To Be Published
Title: Dimer structure of the MATE family multidrug resistance transporter 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
B: Aq128


Theoretical massNumber of molelcules
Total (without water)105,2342
Polymers105,2342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, The homodimeric state of Aq128 was verified by CN-PAGE and SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-33 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.100, 73.600, 101.800
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aq128


Mass: 52617.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 8
Details: 0.1 M Tris 0.2 M ammonium sulphate 30% PEG 500 MME(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: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 23304 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 79.62 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.074 / Rrim(I) all: 0.15 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.712 / Num. unique obs: 2291 / CC1/2: 0.731 / Rpim(I) all: 0.442 / Rrim(I) all: 0.84 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FV6

6fv6


Resolution: 3→19.926 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.17
RfactorNum. reflection% reflection
Rfree0.287 1165 5 %
Rwork0.2648 --
obs0.2659 23277 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→19.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 0 0 6908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037107
X-RAY DIFFRACTIONf_angle_d0.6319666
X-RAY DIFFRACTIONf_dihedral_angle_d12.9994115
X-RAY DIFFRACTIONf_chiral_restr0.0391134
X-RAY DIFFRACTIONf_plane_restr0.0041160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.13620.37861420.34512711X-RAY DIFFRACTION98
3.1362-3.30090.33211460.33162780X-RAY DIFFRACTION99
3.3009-3.50660.34271470.31382773X-RAY DIFFRACTION99
3.5066-3.77570.31061440.28342737X-RAY DIFFRACTION99
3.7757-4.15260.29921440.26892748X-RAY DIFFRACTION99
4.1526-4.74640.2651460.25112776X-RAY DIFFRACTION99
4.7464-5.95330.27721460.26762769X-RAY DIFFRACTION99
5.9533-19.92620.24841500.222818X-RAY DIFFRACTION98

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