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Yorodumi- PDB-5wkx: Barium sites in the structure of a resting acid sensing ion channel -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wkx | ||||||||||||
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Title | Barium sites in the structure of a resting acid sensing ion channel | ||||||||||||
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: 4.034 Å | ||||||||||||
Authors | Yoder, N. / Gouaux, E. | ||||||||||||
Funding support | United States, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wkx.cif.gz | 250.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wkx.ent.gz | 195.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wkx_validation.pdf.gz | 676.9 KB | Display | wwPDB validaton report |
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Full document | 5wkx_full_validation.pdf.gz | 690.8 KB | Display | |
Data in XML | 5wkx_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 5wkx_validation.cif.gz | 59.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wkx ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wkx | HTTPS FTP |
-Related structure data
Related structure data | 5wkyC 6cmcC 5wkuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 150 mM NaCl, 29% PEG 400, 20 mM BaCl2. Crystal soaked in 50 mM BaCl2 prior to freezing. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.93725 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.93725 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 33891 / % possible obs: 99.5 % / Redundancy: 6.89 % / CC1/2: 0.999 / Net I/σ(I): 8.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WKU Resolution: 4.034→49.656 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.96 / 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: 4.034→49.656 Å
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Refine LS restraints |
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LS refinement shell |
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