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- PDB-5yua: Crystal structure of voltage-gated sodium channel NavAb in high-p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yua | ||||||
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Title | Crystal structure of voltage-gated sodium channel NavAb in high-pH 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. / Shimomura, T. / Fujiyoshi, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb. Authors: Irie, K. / Haga, Y. / Shimomura, T. / 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 | ![]() | 137.2 KB | Display | ![]() |
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PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yubC ![]() 5yucC ![]() 3rvyS 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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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: 31382.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Sugar |
-Non-polymers , 4 types, 17 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/1N7.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1N7.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||
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#4: Chemical | ChemComp-1N7 / | ||
#5: Chemical | ChemComp-PX4 / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.42 Å3/Da / Density % sol: 80.85 % / Description: pyramidal shape |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 11% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl pH 8.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→31.47 Å / Num. obs: 20186 / % possible obs: 87.68 % / Redundancy: 9.1 % / Biso Wilson estimate: 60.9798776849 Å2 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.087 / Net I/σ(I): 14.02 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.3136 / Num. unique obs: 505 / Rpim(I) all: 1.074 / % possible all: 25.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RVY Resolution: 2.8008556672→31.4605001582 Å / SU ML: 0.447921114119 / Cross valid method: FREE R-VALUE / σ(F): 1.33590617468 / Phase error: 30.3553703658 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: 88.7405017713 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8008556672→31.4605001582 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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