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Yorodumi- PDB-7jk8: EmrE S64V mutant bound to tetra(4-fluorophenyl)phosphonium at pH 5.8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jk8 | ||||||
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Title | EmrE S64V mutant bound to tetra(4-fluorophenyl)phosphonium at pH 5.8 | ||||||
Components | Multidrug SMR transporter | ||||||
Keywords | MEMBRANE PROTEIN / Small multidrug resistance protein / Antiporter / Drug efflux pump | ||||||
Function / homology | Function and homology information EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / glycine betaine transport / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / glycine betaine transport / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity / transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / membrane => GO:0016020 / response to xenobiotic stimulus / DNA damage response / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLID-STATE NMR / molecular dynamics | ||||||
Authors | Shcherbakov, A.A. / Hisao, G. / Mandala, V.S. / Thomas, N.E. / Soltani, M. / Salter, E.A. / Davis Jr., J.H. / Henzler-Wildman, K.A. / Hong, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers. Authors: Shcherbakov, A.A. / Hisao, G. / Mandala, V.S. / Thomas, N.E. / Soltani, M. / Salter, E.A. / Davis Jr., J.H. / Henzler-Wildman, K.A. / Hong, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jk8.cif.gz | 638.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jk8.ent.gz | 539.6 KB | Display | PDB format |
PDBx/mmJSON format | 7jk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/7jk8 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jk8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11975.331 Da / Num. of mol.: 2 / Mutation: S64V Source method: isolated from a genetically manipulated source Details: Asymmetric homodimer - chemical shift data for two chains are different. Source: (gene. exp.) Escherichia coli (E. coli) Gene: emrE, emrE_2, BvCmsNSNP036_03582, D3821_21360, D9G11_17095, EYY27_16395, NCTC12650_04038, SAMEA3752559_04448 Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X7QID6, UniProt: P23895*PLUS #2: Chemical | ChemComp-VCJ / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.07 M / Label: sample_conditions_1 / pH: 5.8 / Pressure: 1 atm / Temperature: 285 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 160 / Conformers submitted total number: 10 |