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Open data
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Basic information
Entry | Database: PDB / ID: 4pa9 | |||||||||
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Title | Structure of NavMS in complex with channel blocking compound | |||||||||
![]() | 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: 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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Remark 0 | : statistics at the very beginning when nothing is done yet |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.8 KB | Display | ![]() |
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PDB format | ![]() | 131.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cbcC ![]() 4oxsC ![]() 4p2zC ![]() 4p30C ![]() 4p9oC ![]() 4p9pC ![]() 4pa3C ![]() 4pa4C ![]() 4pa6C ![]() 4pa7C ![]() 3zjzS C: citing same article ( S: Starting model for refinement |
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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 Details: pore and C-terminal domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-2CV / #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Nonpolymer details | THE BROMINE ION IS FROM THE COMPOUND 2-(4-BROMOPHENYL)-1-(5-(4-CHLOROPHENYL)-1H-IMIDAZOL-2-YL) ...THE BROMINE ION IS FROM THE COMPOUND 2-(4-BROMOPHENY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.9 % / 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, pH 8.0, 34 % PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013 |
Radiation | Monochromator: channel cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.43→45.42 Å / Num. obs: 14756 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 31 % / Biso Wilson estimate: 81.49 Å2 / Rmerge(I) obs: 0.44 / Rsym value: 0.076 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.43→3.7 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 4.3 / % possible all: 96.8 |
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Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() Starting model: starting model 3ZJZ Resolution: 3.43→45.42 Å / Cor.coef. Fo:Fc: 0.7658 / Cor.coef. Fo:Fc free: 0.7933 / SU R Cruickshank DPI: 1.057 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.039 / SU Rfree Blow DPI: 0.449 / SU Rfree Cruickshank DPI: 0.456
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Displacement parameters | Biso mean: 61.74 Å2
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Refine analyze | Luzzati coordinate error obs: 1.018 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.43→45.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.43→3.71 Å / Total num. of bins used: 7
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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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