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Yorodumi- PDB-8ctu: Crystal structure of a K+ selective NaK mutant (NaK2K) at Room te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ctu | ||||||||||||||||||||||||||||||
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Title | Crystal structure of a K+ selective NaK mutant (NaK2K) at Room temperature | ||||||||||||||||||||||||||||||
Components | Potassium channel protein | ||||||||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Potassium ion channel / anomalous / room temperature | ||||||||||||||||||||||||||||||
Function / homology | Two pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / membrane / beta-D-galactopyranose / : / Potassium channel protein Function and homology information | ||||||||||||||||||||||||||||||
Biological species | Bacillus cereus m1550 (bacteria) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 8ctu.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ctu.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ctu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8ctu ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ctu | HTTPS FTP |
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-Related structure data
Related structure data | 8ctnC 8ctsC 8cttC 8ctvC 8ctwC 8ctxC 8cu1C 8cu2C 8cu3C 8cu4C 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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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10640.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus m1550 (bacteria) / Gene: bcere0011_5790 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: C2R3K4 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose |
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#5: Sugar | ChemComp-GAL / |
-Non-polymers , 3 types, 45 molecules
#3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.52 Å3/Da / Density % sol: 51.18 % |
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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: 292 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.4938 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4938 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 49726 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.53 Å2 / Rsym value: 0.087 / Net I/σ(I): 21.392 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.156 / Num. unique obs: 2467 / CC1/2: 0.743 / Rsym value: 0.563 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Room temperature monochromatic NaK2K structure Resolution: 1.65→48.73 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.8442 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: 26.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→48.73 Å
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Refine LS restraints |
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LS refinement shell |
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