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Yorodumi- PDB-6fv7: Dimer structure of the MATE family multidrug resistance transport... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fv7 | ||||||||||||
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Title | Dimer 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: 3.7 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: Dimer 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 | 6fv7.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fv7.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fv7_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 6fv7_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 6fv7_validation.xml.gz | 30 KB | Display | |
Data in CIF | 6fv7_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/6fv7 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/6fv7 | HTTPS FTP |
-Related structure data
Related structure data | 6fv6S 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.: 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % |
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Crystal grow | Temperature: 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) |
-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: Dec 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→19.884 Å
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Refine LS restraints |
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LS refinement shell |
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