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- PDB-6fv7: Dimer structure of the MATE family multidrug resistance transport... -

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Basic information

Entry
Database: PDB / ID: 6fv7
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 VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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: Dimer 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
B: Aq128


Theoretical massNumber of molelcules
Total (without water)105,2342
Polymers105,2342
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Dimer in solution confirmed by CN-PAGE and SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-18 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.600, 116.500, 142.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6
Details: 0.1 M Sodium chloride 0.1 M Magnesium chloride 0.1 M MES 40 % PEG 200 (v/v)

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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: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→20 Å / Num. obs: 13317 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 120.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.107 / Rrim(I) all: 0.257 / Net I/σ(I): 5
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 6 % / Rmerge(I) obs: 1.109 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1314 / CC1/2: 0.79 / Rpim(I) all: 0.482 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FV6

6fv6


Resolution: 3.7→19.884 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.05
RfactorNum. reflection% reflection
Rfree0.3592 1216 4.96 %
Rwork0.3271 --
obs0.3288 13292 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→19.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6571 0 0 0 6571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026754
X-RAY DIFFRACTIONf_angle_d0.5389177
X-RAY DIFFRACTIONf_dihedral_angle_d10.2833892
X-RAY DIFFRACTIONf_chiral_restr0.0381083
X-RAY DIFFRACTIONf_plane_restr0.0041092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.84720.34551430.40962619X-RAY DIFFRACTION100
3.8472-4.02090.45741370.40662618X-RAY DIFFRACTION99
4.0209-4.2310.40111340.40012590X-RAY DIFFRACTION100
4.231-4.49320.44771310.36742605X-RAY DIFFRACTION99
4.4932-4.83550.34921400.34122590X-RAY DIFFRACTION99
4.8355-5.31370.33621340.33882582X-RAY DIFFRACTION99
5.3137-6.06340.31781350.35162600X-RAY DIFFRACTION99
6.0634-7.56850.40541350.31292575X-RAY DIFFRACTION99
7.5685-19.88420.291270.23172532X-RAY DIFFRACTION96

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