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Open data
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Basic information
Entry | Database: PDB / ID: 4lto | ||||||
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Title | Bacterial sodium channel in high calcium, I222 space group | ||||||
![]() | Ion transport protein | ||||||
![]() | TRANSPORT PROTEIN / cation channel fold / coiled coil sodium channel / plasma membrane | ||||||
Function / homology | ![]() voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shaya, D. / Findeisen, F. / Abderemane-Ali, F. / Arrigoni, C. / Wong, S. / Reddy Nurva, S. / Loussouarn, G. / Minor, D.L. | ||||||
![]() | ![]() Title: Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels. Authors: Shaya, D. / Findeisen, F. / Abderemane-Ali, F. / Arrigoni, C. / Wong, S. / Nurva, S.R. / Loussouarn, G. / Minor, D.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.7 KB | Display | ![]() |
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PDB format | ![]() | 179.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.1 KB | Display | ![]() |
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Full document | ![]() | 510.4 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ltpC ![]() 4ltqC ![]() 4ltrC ![]() 3rvyS ![]() 4dxwS ![]() 4ekwS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper:
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Components
#1: Protein | Mass: 17463.344 Da / Num. of mol.: 4 Fragment: Pore and cytoplasmic domains (UNP residues 143-288) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.93 Å3/Da / Density % sol: 82.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 200 mM calcium chloride, 30% PEG400, 100 mM sodium acetate, pH 5.0, 0.5 M TMAO, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2011 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 3.46→50 Å / Num. all: 24208 / Num. obs: 22804 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.46→3.65 Å / Redundancy: 2.8 % / Rmerge(I) obs: 3.074 / Mean I/σ(I) obs: 0.3 / % possible all: 72.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3RVY, 4DXW, AND 4EKW Resolution: 3.46→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 56.107 / SU ML: 0.399 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.713 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 173.018 Å2
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Refinement step | Cycle: LAST / Resolution: 3.46→15 Å
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Refine LS restraints |
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