[English] 日本語
Yorodumi- PDB-5wky: Bromide sites in the structure of an acid sensing ion channel in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wky | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Bromide sites in the structure of an acid sensing ion channel in a resting state | ||||||||||||
Components | Acid-sensing ion channel 1 | ||||||||||||
Keywords | TRANSPORT PROTEIN / Ion channel / ASIC / ASIC1a / Sodium channel / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||||||||
Authors | Yoder, N. / Gouaux, E. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: PLoS ONE / Year: 2018 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wky.cif.gz | 250 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wky.ent.gz | 195.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wky_validation.pdf.gz | 700.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5wky_full_validation.pdf.gz | 712.9 KB | Display | |
Data in XML | 5wky_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 5wky_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wky ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wky | HTTPS FTP |
-Related structure data
Related structure data | 5wkxC 6cmcC 5wkuS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Production host: Homo sapiens (human) / References: UniProt: Q1XA76 #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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.37 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9191 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|