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- PDB-8cu4: Structure of a K+ selective NaK mutant (NaK2K, Laue diffraction) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cu4 | ||||||||||||||||||||||||||||||
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Title | Structure of a K+ selective NaK mutant (NaK2K, Laue diffraction) in the presence of an electric field of ~0.8MV/cm along the crystallographic z axis, 1us, with eightfold extrapolation of structure factor differences | ||||||||||||||||||||||||||||||
![]() | Potassium channel protein | ||||||||||||||||||||||||||||||
![]() | MEMBRANE PROTEIN / Potassium ion channel / EFX / electric field / 1000ns | ||||||||||||||||||||||||||||||
Function / homology | Two pore domain potassium channel / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / Potassium channel domain / Ion channel / membrane / : / Potassium channel domain-containing protein![]() | ||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
![]() | Lee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Direct visualization of electric field-stimulated ion conduction in a potassium channel Authors: Lee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 90.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.5 MB | Display | ![]() |
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Full document | ![]() | 5.4 MB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ctnSC ![]() 8ctsC ![]() 8cttC ![]() 8ctuC ![]() 8ctvC ![]() 8ctwC ![]() 8ctxC ![]() 8cu1C ![]() 8cu2C ![]() 8cu3C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10640.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM KCl, 200mM potassium citrate tribasic monohydrate, 100mM MES (pH 6.0 or 6.5), 56%-68% 2-methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 283.15 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Mar 21, 2020 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→100 Å / Num. obs: 10640 / % possible obs: 75.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.08 Å2 Data reduction details: Data were indexed, integrated, scaled, and merged in Precognition and Epinorm. These programs apply a cutoff during scaling, omitting weak reflections. As a result, F/sigF is ...Data reduction details: Data were indexed, integrated, scaled, and merged in Precognition and Epinorm. These programs apply a cutoff during scaling, omitting weak reflections. As a result, F/sigF is high (F/sigF = 40 in the high resolution shell) and completeness low relative to what is observed for conventional monochromatic software. Rmerge(I) obs: 0.078 / Net I/σ(I): 42.67 | |||||||||
Reflection shell | Resolution: 2→2.09 Å / Rmerge F obs: 0.046 / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 7.59 / Num. unique obs: 532 / % possible all: 30.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8CTN Resolution: 2.01→27.59 Å / SU ML: 0.4294 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 43.4162 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.05 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→27.59 Å
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Refine LS restraints |
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LS refinement shell |
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