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Open data
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Basic information
Entry | Database: PDB / ID: 5hkd | ||||||
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Title | Bacterial sodium channel neck 7G mutant | ||||||
![]() | Ion transport protein | ||||||
![]() | TRANSPORT PROTEIN / Bacterial sodium channel | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 108.5 KB | Display | ![]() |
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PDB format | ![]() | 82.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.6 KB | Display | ![]() |
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Full document | ![]() | 482.9 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hj8C ![]() 5hk6C ![]() 5hk7C ![]() 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: 17076.822 Da / Num. of mol.: 4 / Fragment: UNP residues 143-288 / Mutation: A112G, E113G, D114G, A115G, K116G, R117G, I118G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.99 Å3/Da / Density % sol: 79.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 30% PEG400, 20 mM MES, pH 5.8 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→68.6 Å / Num. obs: 18097 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Net I/σ(I): 6.22 |
Reflection shell | Highest resolution: 3.8 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4LTO Resolution: 3.8→15 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / ESU R: 4.035 / ESU R Free: 0.606
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 162.235 Å2
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Refinement step | Cycle: 1 / Resolution: 3.8→15 Å
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Refine LS restraints |
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