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Open data
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Basic information
Entry | Database: PDB / ID: 5hk7 | ||||||
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Title | Bacterial sodium channel pore, 2.95 Angstrom resolution | ||||||
![]() | Ion transport protein | ||||||
![]() | TRANSPORT PROTEIN / Bacterial sodium channel pore | ||||||
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. / Rohaim, A. / Minor, D.L. | ||||||
![]() | ![]() Title: Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation. Authors: Arrigoni, C. / Rohaim, A. / Shaya, D. / Findeisen, F. / Stein, R.A. / Nurva, S.R. / Mishra, S. / Mchaourab, H.S. / 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 | ![]() | 129.5 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hj8C ![]() 5hk6C ![]() 5hkdC ![]() 5iwnC ![]() 5iwoC ![]() 4ltoS 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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Components
#1: Protein | Mass: 17463.344 Da / Num. of mol.: 4 / Fragment: UNP residues 143-288 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-VVA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.34 Å3/Da / Density % sol: 83.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 27% PEG300, 100 mM sodium acetate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→80.26 Å / Num. all: 43185 / Num. obs: 42643 / % possible obs: 99.2 % / Redundancy: 8.5 % / Rsym value: 0.201 / Net I/σ(I): 6.7 |
Reflection shell | Highest resolution: 2.95 Å / Rsym value: 2.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4LTO Resolution: 2.95→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.808 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.243 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.41 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→15 Å
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Refine LS restraints |
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