+Open data
-Basic information
Entry | Database: PDB / ID: 6v8y | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a Sodium Potassium ion Channel | ||||||
Components | Potassium channel protein | ||||||
Keywords | MEMBRANE PROTEIN / ion channel | ||||||
Function / homology | Two pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / membrane / : / Transporter Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Roy, R. / Weiss, K.L. / Coates, L. | ||||||
Citation | Journal: Iucrj / Year: 2021 Title: Structural plasticity of the selectivity filter in a nonselective ion channel. Authors: Roy, R.N. / Hendriks, K. / Kopec, W. / Abdolvand, S. / Weiss, K.L. / de Groot, B.L. / Lange, A. / Sun, H. / Coates, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6v8y.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6v8y.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8y ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8y | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ahyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 10706.538 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) Gene: A9485_19160, B4155_3291, BACERE00184_02078, CN419_22740, CN950_06075, CN980_22870, COI98_17615, COK18_26145, CON37_12595 Production host: Escherichia coli (E. coli) / References: UniProt: A0A164U772 #2: Chemical | ChemComp-MPD / ( #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: See paper for details |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→38.34 Å / Num. obs: 49908 / % possible obs: 97.1 % / Redundancy: 7.04 % / CC1/2: 0.999 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.53→1.58 Å / Num. unique obs: 2568 / CC1/2: 0.678 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AHY Resolution: 1.53→38.322 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.37
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→38.322 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|