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- PDB-8h9x: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h9x | |||||||||
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Title | Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in sodium ion condition | |||||||||
![]() | Ion transport protein | |||||||||
![]() | MEMBRANE PROTEIN / ion channel | |||||||||
Function / homology | ![]() voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Irie, K. / Oda, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Authors: Irie, K. / Oda, Y. / Sumikama, T. / Oshima, A. / Fujiyoshi, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.6 KB | Display | ![]() |
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PDB format | ![]() | 105.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h9oC ![]() 8h9wC ![]() 8h9yC ![]() 8ha1C ![]() 8ha2C ![]() 5yucS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 3 molecules A![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 31412.252 Da / Num. of mol.: 1 / Mutation: N49K, L176Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar |
-Non-polymers , 4 types, 24 molecules ![](data/chem/img/1N7.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-1N7 / | ||||
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#4: Chemical | ChemComp-PX4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.54 Å3/Da / Density % sol: 81.18 % / Description: Pyramidal shape |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→29.31 Å / Num. obs: 11812 / % possible obs: 91.84 % / Redundancy: 83.4 % / Biso Wilson estimate: 53.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.08 |
Reflection shell | Resolution: 3.4→3.5 Å / Num. unique obs: 449 / CC1/2: 0.701 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5yuc Resolution: 3.4→29.31 Å / SU ML: 0.2425 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1838 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: 69.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→29.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.7483917755 Å / Origin y: -16.6218474306 Å / Origin z: 25.7677203389 Å
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Refinement TLS group | Selection details: all |