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- PDB-4cbc: Open-form NavMS Sodium Channel Pore (with C-terminal Domain) afte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cbc | ||||||
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Title | Open-form NavMS Sodium Channel Pore (with C-terminal Domain) after thallium soak | ||||||
![]() | ION TRANSPORT PROTEIN![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bagneris, C. / Naylor, C.E. / Wallace, B.A. | ||||||
![]() | ![]() 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.M. / 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 | ![]() | 170.7 KB | Display | ![]() |
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PDB format | ![]() | 136.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4oxsC ![]() 4p2zC ![]() 4p30C ![]() 4p9oC ![]() 4p9pC ![]() 4pa3C ![]() 4pa4C ![]() 4pa6C ![]() 4pa7C ![]() 4pa9C ![]() 4bha ![]() 4cal ![]() 4cbd 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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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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | ![]() Mass: 16836.502 Da / Num. of mol.: 4 / Fragment: PORE AND CTD, RESIDUES 130-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-2CV / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | ![]() Sequence details | CONSTRUCT CONSISTS OF PORE AND C-TERMINAL DOMAIN ONLY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.5 Å3/Da / Density % sol: 83.5 % / Description: NONE |
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Crystal grow![]() | pH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012 / Details: MIRRORS |
Radiation | Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.67→45.47 Å / Num. obs: 30860 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.67→2.79 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.7 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4BHA ![]() 4bha Resolution: 2.664→45.469 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 34.16 / Stereochemistry target values: ML
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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: 55.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.664→45.469 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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