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Open data
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Basic information
Entry | Database: PDB / ID: 5bzb | |||||||||
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Title | NavMs voltage-gated sodium channel pore and C-terminal domain | |||||||||
![]() | Ion transport protein![]() | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Naylor, C.E. / Bagneris, C. / Wallace, B.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of ion permeability in a voltage-gated sodium channel. Authors: Naylor, C.E. / Bagneris, C. / DeCaen, P.G. / Sula, A. / Scaglione, A. / Clapham, D.E. / Wallace, B.A. #1: ![]() Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels. Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W. / Wallace, B.A. #2: ![]() Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.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 | ![]() | 176.8 KB | Display | ![]() |
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PDB format | ![]() | 138.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4x88C ![]() 4x89C ![]() 4x8aC ![]() 3zjzS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 16836.502 Da / Num. of mol.: 4 Fragment: navms pore and c-terminal domain, UNP residues 130-274 Source method: isolated from a genetically manipulated source Details: c-terminal is not visible in the electron density / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-2CV / #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.58 Å3/Da / Density % sol: 83.77 % / Description: flat plates |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1m na3citrate, 0.1m tris ph 8.0, 34% peg 400 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2013 |
Radiation | Monochromator: si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→57.81 Å / Num. all: 30179 / Num. obs: 30149 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 40.38 Å2 / Rmerge(I) obs: 0.245 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3ZJZ Resolution: 2.7→57.81 Å / Cor.coef. Fo:Fc: 0.9003 / Cor.coef. Fo:Fc free: 0.8265 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.19
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Displacement parameters | Biso mean: 46.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.314 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.7→57.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.79 Å / Total num. of bins used: 15
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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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