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- PDB-5wky: Bromide sites in the structure of an acid sensing ion channel in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wky | ||||||||||||
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Title | Bromide sites in the structure of an acid sensing ion channel in a resting state | ||||||||||||
![]() | Acid-sensing ion channel 1 | ||||||||||||
![]() | TRANSPORT PROTEIN / Ion channel / ASIC / ASIC1a / Sodium channel / MEMBRANE PROTEIN | ||||||||||||
Function / homology | ![]() pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / protein homotrimerization / sodium ion transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yoder, N. / Gouaux, E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Divalent cation and chloride ion sites of chicken acid sensing ion channel 1a elucidated by x-ray crystallography. Authors: Yoder, N. / Gouaux, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250 KB | Display | ![]() |
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PDB format | ![]() | 195.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wkxC ![]() 6cmcC ![]() 5wkuS 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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Unit cell |
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Components
#1: Protein | Mass: 50241.160 Da / Num. of mol.: 3 / Fragment: UNP residues 25-463 Source method: isolated from a genetically manipulated source Details: FRAGMENT: 25-463 / Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Chemical | ChemComp-BA / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 100 mM NaCl, 29% PEG 400, 5 mM BaCl2. Crystal soaked in 150 mM NaBr prior to freezing. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 |
Reflection | Resolution: 4→45 Å / Num. obs: 38333 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 1 / Net I/σ(I): 9.46 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WKU Resolution: 4→43.15 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.81 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→43.15 Å
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Refine LS restraints |
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LS refinement shell |
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