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Open data
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Basic information
Entry | Database: PDB / ID: 8a7x | |||||||||||||||
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Title | NaK C-DI F92A mutant soaked in Cs+ | |||||||||||||||
![]() | Potassium channel protein | |||||||||||||||
![]() | TRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / identical protein binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Minniberger, S. / Plested, A.J.R. | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors. Authors: Minniberger, S. / Abdolvand, S. / Braunbeck, S. / Sun, H. / Plested, A.J.R. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.2 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oorC ![]() 7oouC ![]() 7ophC ![]() 7oq1C ![]() 7oq2C ![]() 7pa0C ![]() 8a35C ![]() 3e86S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
#1: Protein | Mass: 10659.609 Da / Num. of mol.: 2 / Mutation: D66C G67- N68D F69I F92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: BC_0669 / Plasmid: pQE60 / Production host: ![]() ![]() #2: Chemical | ChemComp-CS / #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % / Description: thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200 mM CsCl 100 mM Tris-HCl pH 8.0, 63% MPD (2-Methyl-2,4-pentanediol racemate) - soaked in 90 mM CsCl, 100 mM Kryptofix-222, 50% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.12 Å / Num. obs: 22957 / % possible obs: 96.07 % / Redundancy: 2.2 % / Biso Wilson estimate: 44.36 Å2 / CC1/2: 0.936 / CC star: 0.983 / Rmerge(I) obs: 0.1228 / Rpim(I) all: 0.09434 / Net I/σ(I): 44.22 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.9152 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2360 / CC1/2: 0.392 / CC star: 0.75 / Rpim(I) all: 0.7146 / % possible all: 96.97 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 63.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.12 Å
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Refine LS restraints |
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LS refinement shell |
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