+Open data
-Basic information
Entry | Database: PDB / ID: 6u9y | |||||||||
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Title | Wild-type MthK pore in 11 mM K+ | |||||||||
Components | Calcium-gated potassium channel MthK | |||||||||
Keywords | TRANSPORT PROTEIN / Potassium ion channel MthK | |||||||||
Function / homology | Function and homology information monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Posson, D.J. / Nimigean, C.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Selectivity filter ion binding affinity determines inactivation in a potassium channel. Authors: Boiteux, C. / Posson, D.J. / Allen, T.W. / Nimigean, C.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u9y.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u9y.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 6u9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/6u9y ftp://data.pdbj.org/pub/pdb/validation_reports/u9/6u9y | HTTPS FTP |
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-Related structure data
Related structure data | 6u9pC 6u9tC 6u9zC 3ldcS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8979.500 Da / Num. of mol.: 1 / Fragment: UNP residues 18-99 / Mutation: UNP residues 18-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564 | ||||||
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#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-HEZ / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1:1 protein (in 100 mM sodium chloride, 1 mM potassium chloride, 10 mM MOPS, pH 8.0) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-NaOH, 10 mM potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.9 Å / Num. obs: 8824 / % possible obs: 99.81 % / Redundancy: 24.9 % / Biso Wilson estimate: 23.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1446 / Rpim(I) all: 0.02937 / Rrim(I) all: 0.1476 / Net I/σ(I): 22.59 |
Reflection shell | Resolution: 1.8→1.868 Å / Redundancy: 25 % / Rmerge(I) obs: 3.326 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 838 / CC1/2: 0.613 / Rpim(I) all: 0.6733 / Rrim(I) all: 3.395 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LDC Resolution: 1.8→31.9 Å / SU ML: 0.1813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6811
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→31.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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