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Open data
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Basic information
Entry | Database: PDB / ID: 4pa3 | |||||||||
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Title | Structure of NavMS in complex with channel blocking compound | |||||||||
![]() | Ion transport protein | |||||||||
![]() | TRANSPORT PROTEIN / channel blocking compound / sodium channel / pore / membrane protein | |||||||||
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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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 KB | Display | ![]() |
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PDB format | ![]() | 131 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cbcC ![]() 4oxsC ![]() 4p2zC ![]() 4p30C ![]() 4p9oC ![]() 4p9pC ![]() 4pa4C ![]() 4pa6C ![]() 4pa7C ![]() 4pa9C ![]() 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 on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 36 molecules ![](data/chem/img/2CV.gif)
![](data/chem/img/12P.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/12P.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-2CV / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE BROMINE ION IS FROM THE COMPOUND 3-(4-BROMOPHENYL)PROPANAMINE THAT IS PRESENT AT TOO LOW ...THE BROMINE ION IS FROM THE COMPOUND 3-(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 Ctriate, 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: Dec 6, 2013 |
Radiation | Monochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918401 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→45.54 Å / Num. obs: 17145 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 101.61 Å2 / Rmerge(I) obs: 0.204 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 3.25→3.51 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.1 / % possible all: 94.3 |
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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: 3.25→45.54 Å / Cor.coef. Fo:Fc: 0.8761 / Cor.coef. Fo:Fc free: 0.8875 / SU R Cruickshank DPI: 0.534 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.522 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.313
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Displacement parameters | Biso mean: 61.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.64 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.25→45.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.45 Å / Total num. of bins used: 9
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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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