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Yorodumi- PDB-6o6j: Crystal structure of the LjCASTOR gating ring in the Ca2+ and Na+... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o6j | ||||||||||||
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Title | Crystal structure of the LjCASTOR gating ring in the Ca2+ and Na+ condition | ||||||||||||
Components | Ion channel CASTOR | ||||||||||||
Keywords | TRANSPORT PROTEIN / calcium channel / RCK domain / gating ring / CASTOR / membrane protein | ||||||||||||
Function / homology | CASTOR/POLLUX/SYM8 ion channel, conserved domain / Ion channel CASTOR/POLLUX/SYM8-like / Castor and Pollux, part of voltage-gated ion channel / monoatomic ion transmembrane transport / nuclear membrane / Ion channel CASTOR Function and homology information | ||||||||||||
Biological species | Lotus japonicus (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||||||||
Authors | Jiang, Y. / Kim, S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2019 Title: Ca2+-regulated Ca2+channels with an RCK gating ring control plant symbiotic associations. Authors: Kim, S. / Zeng, W. / Bernard, S. / Liao, J. / Venkateshwaran, M. / Ane, J.M. / Jiang, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o6j.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o6j.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 6o6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/6o6j ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o6j | HTTPS FTP |
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-Related 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: 61956.867 Da / Num. of mol.: 1 / Fragment: gating ring (UNP residues 312-853) Source method: isolated from a genetically manipulated source Details: Jean-Michel Ane, University of Wisconsin - Madison, Madison, WI 53706, USA. Source: (gene. exp.) Lotus japonicus (plant) / Gene: CASTOR / Variant: Gifu / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q5H8A6 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.47 % / Description: a thin rectangular prism with smooth edges |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 21% w/v PEG550 MME, 50 mM magnesium acetate, 100 mM Tris, pH 8.2 PH range: 7.5-8.5 / Temp details: 293 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.94936 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2013 |
Radiation | Monochromator: Rosenbaum-Rock double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94936 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 160841 / % possible obs: 98.75 % / Redundancy: 5 % / Biso Wilson estimate: 17.93 Å2 / Net I/σ(I): 34.54 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 1.983 / Num. unique obs: 7449 / CC1/2: 0.405 / Rpim(I) all: 0.671 / Rrim(I) all: 1.382 / Rsym value: 1.201 / Χ2: 1.149 / % possible all: 90.21 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→39.6 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4919
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→39.6 Å
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Refine LS restraints |
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LS refinement shell |
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