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- PDB-4p9o: Complex of Voltage-gated ion channel in a the presence of channel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4p9o | |||||||||
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Title | Complex of Voltage-gated ion channel in a the presence of channel blocking compound | |||||||||
![]() | Ion transport protein | |||||||||
![]() | TRANSPORT PROTEIN / ion channel / membrane protein / channel blocker | |||||||||
Function / homology | ![]() voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Naylor, C.E. / Bagneris, C. / Wallace, B.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism. Authors: Bagneris, C. / DeCaen, P.G. / Naylor, C.E. / Pryde, D.C. / Nobeli, I. / 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 | ![]() | 171.8 KB | Display | ![]() |
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PDB format | ![]() | 136.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cbcC ![]() 4oxsC ![]() 4p2zC ![]() 4p30C ![]() 4p9pC ![]() 4pa3C ![]() 4pa4C ![]() 4pa6C ![]() 4pa7C ![]() 4pa9C ![]() 4cbd 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16836.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-2CV / #3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | Nonpolymer details | THE BROMINE ION IS PART OF THE MOLECULE 2-(4-BROMOPHENYL)-1-(5-(4-CHLOROPHENYL)-1H-IMIDAZOL-2-YL) ...THE BROMINE ION IS PART OF THE MOLECULE 2-(4-BROMOPHENY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.78 % / Description: Flat rectangular plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M sodium citrate, 0.1 M Tris, 34% PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2013 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→45.24 Å / Num. obs: 24368 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.89→3.07 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.714 / Net I/σ(I) obs: 3.6 / % possible all: 99 |
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Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.89→32.91 Å / Cor.coef. Fo:Fc: 0.8963 / Cor.coef. Fo:Fc free: 0.8584 / SU R Cruickshank DPI: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.353 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.265
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Displacement parameters | Biso mean: 61.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.393 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.89→32.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.89→3.02 Å / Total num. of bins used: 12
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Refinement TLS params. | T11: -0.304 Å2 / T22: 0.304 Å2 / T33: -0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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