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Yorodumi- PDB-6fv6: Monomer structure of the MATE family multidrug resistance transpo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fv6 | ||||||||||||
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Title | Monomer structure of the MATE family multidrug resistance transporter Aq_128 from Aquifex aeolicus in the outward-facing state | ||||||||||||
Components | Aq128 | ||||||||||||
Keywords | MEMBRANE 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 species | Aquifex aeolicus VF5 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||||||||
Authors | Zhao, J. / Safarian, S. / Thielmann, Y. / Xie, H. / Wang, J. / Michel, H. | ||||||||||||
Funding support | Germany, China, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fv6.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fv6.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/6fv6 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/6fv6 | HTTPS FTP |
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-Related structure data
Related structure data | 4mlbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.72 % / Description: plate |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M Tris 1.2 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→19.972 Å
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Refine LS restraints |
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LS refinement shell |
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