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- PDB-8diy: Crystal structure of NavAb L101S as a basis for the human Nav1.7 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8diy | |||||||||||||||
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Title | Crystal structure of NavAb L101S as a basis for the human Nav1.7 Inherited Erythromelalgia F216S mutation | |||||||||||||||
![]() | Ion transport protein | |||||||||||||||
![]() | MEMBRANE PROTEIN / Voltage-gated sodium channel Ion transport protein | |||||||||||||||
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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Wisedchaisri, G. / Gamal El-Din, T.M. / Zheng, N. / Catterall, W.A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for severe pain caused by mutations in the voltage sensors of sodium channel NaV1.7. Authors: Wisedchaisri, G. / Gamal El-Din, T.M. / Powell, N.M. / Zheng, N. / Catterall, W.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8divC ![]() 8diwC ![]() 8dixC ![]() 6mwaS 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
#1: Protein | Mass: 29763.215 Da / Num. of mol.: 1 / Mutation: L101S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RM4018 / Gene: Abu_1752 / Production host: ![]() | ||||||
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#2: Chemical | ChemComp-PX4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.26 Å3/Da / Density % sol: 80.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 1.7-1.8 M Ammonium Sulfate 0.1 M Sodium Citrate pH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2021 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 17973 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 75.31 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.059 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.344 / Num. unique obs: 841 / CC1/2: 0.548 / Rpim(I) all: 0.674 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MWA Resolution: 2.85→41.99 Å / SU ML: 0.4505 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.7437 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→41.99 Å
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Refine LS restraints |
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LS refinement shell |
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