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Yorodumi- PDB-8cu4: Structure of a K+ selective NaK mutant (NaK2K, Laue diffraction) ... -
+Open data
-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 | ||||||||||||||||||||||||||||||
Components | Potassium channel protein | ||||||||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Potassium ion channel / EFX / electric field / 1000ns | ||||||||||||||||||||||||||||||
Function / homology | Two pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / membrane / : / Potassium channel domain-containing protein Function and homology information | ||||||||||||||||||||||||||||||
Biological species | Bacillus cereus (bacteria) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||||||||||||||||||||||||||
Authors | Lee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D. | ||||||||||||||||||||||||||||||
Funding support | United States, 9items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cu4.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cu4.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/8cu4 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/8cu4 | HTTPS FTP |
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-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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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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.) Bacillus cereus (bacteria) / Strain: m1550 / Gene: BCB4264_A0706 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: B7HBV5 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.15 | |||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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