+Open data
-Basic information
Entry | Database: PDB / ID: 6u9z | |||||||||
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Title | Wild-type MthK pore in 6 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: 1.954 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 | 6u9z.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u9z.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 6u9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/6u9z ftp://data.pdbj.org/pub/pdb/validation_reports/u9/6u9z | HTTPS FTP |
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-Related structure data
Related structure data | 6u9pC 6u9tC 6u9yC 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 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: protein (in 100 mM sodium chloride, 1 mM potassium chloride, 10 mM MOPS) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-NaOH, pH 6.75, 5 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: 1.009 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: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.954→44.05 Å / Num. obs: 6986 / % possible obs: 99.66 % / Redundancy: 24.7 % / Biso Wilson estimate: 27.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1864 / Rpim(I) all: 0.03809 / Rrim(I) all: 0.1903 / Net I/σ(I): 15.95 |
Reflection shell | Resolution: 1.954→2.024 Å / Redundancy: 22.5 % / Rmerge(I) obs: 2.1 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 660 / CC1/2: 0.751 / Rpim(I) all: 0.4475 / Rrim(I) all: 2.148 / % possible all: 97.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LDC Resolution: 1.954→44.05 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7274
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.954→44.05 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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