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Yorodumi- PDB-5yub: Crystal structure of voltage-gated sodium channel NavAb E32Q mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yub | ||||||
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Title | Crystal structure of voltage-gated sodium channel NavAb E32Q mutant | ||||||
Components | Ion transport proteinIon transporter | ||||||
Keywords | MEMBRANE PROTEIN / ion channel | ||||||
Function / homology | Function and homology information monoatomic cation channel activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arcobacter butzleri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.40003993335 Å | ||||||
Authors | Irie, K. / Shimomura, T. / Fujiyoshi, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: FEBS Lett. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yub.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yub.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yub ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yub | HTTPS FTP |
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-Related structure data
Related structure data | 5yuaSC 5yucC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 31381.221 Da / Num. of mol.: 1 / Mutation: E32Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (bacteria) / Gene: SAMEA4475700_01771 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239WB15, UniProt: A8EVM5*PLUS |
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#2: Chemical | ChemComp-CA / |
#3: Sugar | ChemComp-LMT / |
#4: Chemical | ChemComp-1N7 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.51 Å3/Da / Density % sol: 81.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Nov 5, 2013 |
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→41.07 Å / Num. obs: 11773 / % possible obs: 86.42 % / Redundancy: 13.9 % / Biso Wilson estimate: 25.3055302345 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.0689 / Net I/σ(I): 14.86 |
Reflection shell | Resolution: 3.4→3.521 Å / Rmerge(I) obs: 1.924 / CC1/2: 0.845 / Rpim(I) all: 0.543 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YUA Resolution: 3.40003993335→41.0616138222 Å / SU ML: 0.287523667776 / Cross valid method: FREE R-VALUE / σ(F): 1.3777448541 / Phase error: 29.4465945713 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: 61.1650526251 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.40003993335→41.0616138222 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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