[English] 日本語
Yorodumi- PDB-4pkx: The structure of a conserved Piezo channel domain reveals a novel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pkx | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of a conserved Piezo channel domain reveals a novel beta sandwich fold | ||||||
Components | Protein C10C5.1, isoform i | ||||||
Keywords | MEMBRANE PROTEIN / Mechanosensitive / channel / piezo | ||||||
Function / homology | Function and homology information positive regulation of brood size / positive regulation of ovulation / flagellated sperm motility / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / monoatomic cation transmembrane transport / response to mechanical stimulus / monoatomic cation channel activity / regulation of membrane potential / cellular response to mechanical stimulus / plasma membrane Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.54 Å | ||||||
Authors | Kamajaya, A. / Kaiser, J. / Lee, J. / Reid, M. / Rees, D.C. | ||||||
Citation | Journal: Structure / Year: 2014 Title: The Structure of a Conserved Piezo Channel Domain Reveals a Topologically Distinct beta Sandwich Fold. Authors: Kamajaya, A. / Kaiser, J.T. / Lee, J. / Reid, M. / Rees, D.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pkx.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pkx.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 4pkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/4pkx ftp://data.pdbj.org/pub/pdb/validation_reports/pk/4pkx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32953.000 Da / Num. of mol.: 1 / Fragment: UNP residues 1327-1608 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C10C5.1, CELE_C10C5.1, T20D3.11 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold / References: UniProt: O01260, UniProt: A0A061ACU2*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 34.51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M phosphate-citrate buffer pH 4.8, 30% PEG3350, and 0.2 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→38.97 Å / Num. obs: 7746 / % possible obs: 93.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2.54→2.68 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 11.2 / % possible all: 75.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.54→33.233 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.57 / 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: 2.54→33.233 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|