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Yorodumi- PDB-8ha1: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ha1 | |||||||||
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Title | Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in sodium ion condition | |||||||||
Components | Ion transport proteinIon transporter | |||||||||
Keywords | MEMBRANE PROTEIN / ion channel | |||||||||
Function / homology | Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / identical protein binding / plasma membrane / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein Function and homology information | |||||||||
Biological species | Aliarcobacter butzleri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Irie, K. / Oda, Y. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ha1.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ha1.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ha1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/8ha1 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/8ha1 | HTTPS FTP |
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-Related structure data
Related structure data | 8h9oC 8h9wC 8h9xC 8h9yC 8ha2C 5yucS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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
#1: Protein | Mass: 31341.174 Da / Num. of mol.: 1 / Mutation: N49K, L176G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aliarcobacter butzleri (bacteria) / Gene: Abu_1752 / Production host: Escherichia coli (E. coli) / References: UniProt: A8EVM5 |
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#2: Sugar |
-Non-polymers , 4 types, 24 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.46 Å3/Da / Density % sol: 80.98 % / 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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: 3.5→29.97 Å / Num. obs: 10747 / % possible obs: 96.59 % / Redundancy: 39.8 % / Biso Wilson estimate: 152.11 Å2 / CC1/2: 1 / Net I/σ(I): 20.78 |
Reflection shell | Resolution: 3.5→3.6 Å / Num. unique obs: 728 / CC1/2: 0.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5yuc Resolution: 3.5→29.91 Å / SU ML: 0.5001 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 33.5777 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: 155.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→29.91 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: 11.7692848821 Å / Origin y: -16.7295059191 Å / Origin z: 25.7358184079 Å
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Refinement TLS group | Selection details: all |