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- PDB-4r50: Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r50 | ||||||
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Title | Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized with Li+ | ||||||
![]() | Potassium channel protein | ||||||
![]() | TRANSPORT PROTEIN / Alpha helical membrane protein / chimera channel | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | De March, M. / Napolitano, L.M.R. / Onesti, S. | ||||||
![]() | ![]() Title: A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels. Authors: Napolitano, L.M. / Bisha, I. / De March, M. / Marchesi, A. / Arcangeletti, M. / Demitri, N. / Mazzolini, M. / Rodriguez, A. / Magistrato, A. / Onesti, S. / Laio, A. / Torre, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85 KB | Display | ![]() |
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PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.9 KB | Display | ![]() |
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Full document | ![]() | 464.3 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r6zC ![]() 4r7cC ![]() 4r8cC ![]() 4raiC ![]() 4ro2C ![]() 3k0dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 22 - 109 / Label seq-ID: 5 - 92
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Details | Tetrameric channel with filter on the 4-fold axis. |
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Components
#1: Protein | Mass: 10626.555 Da / Num. of mol.: 2 / Fragment: residues 20-110 / Mutation: D66E, G67T, N68P, F69P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MPD / ( | #3: Chemical | ChemComp-GLY / #4: Water | ChemComp-HOH / | Nonpolymer details | THE AUTHORS STATE THAT THE LITHIUM ION COULD BE AT THE BRIDGE OF TWO WATER MOLECULES IN THE CENTRAL ...THE AUTHORS STATE THAT THE LITHIUM ION COULD BE AT THE BRIDGE OF TWO WATER MOLECULES IN THE CENTRAL CAVITY OF THE K-CHANNELS. SINCE IT HAS ONLY 3 ELECTRONS THE RESOLUTION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.26 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: 40-70% MPD, 20-100mM Glycine, pH 6.5 - 7.5, VAPOR DIFFUSION, HANGING DROP PH range: 6.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2014 | |||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin | Operator: -H,K,-L / Fraction: 0.4761 | |||||||||||||||
Reflection | Resolution: 2.85→33.81 Å / Num. obs: 4692 / % possible obs: 83 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K0D: chain A without filter and solvent Resolution: 2.85→33.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.387 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.319 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.082 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→33.81 Å
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Refine LS restraints |
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