[English] 日本語
Yorodumi- PDB-6iz3: Structural basis for activity of TRIC counter-ion channels in cal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iz3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural basis for activity of TRIC counter-ion channels in calcium release | |||||||||
Components | Trimeric intracellular cation channel type B-B | |||||||||
Keywords | MEMBRANE PROTEIN | |||||||||
Function / homology | TRIC channel / TRIC channel / potassium channel activity / endoplasmic reticulum membrane / identical protein binding / Trimeric intracellular cation channel type B-B Function and homology information | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.791 Å | |||||||||
Authors | Zeng, Y. / Wang, X.H. / Su, M. / Chen, Y.H. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Structural basis for activity of TRIC counter-ion channels in calcium release. Authors: Wang, X.H. / Su, M. / Gao, F. / Xie, W. / Zeng, Y. / Li, D.L. / Liu, X.L. / Zhao, H. / Qin, L. / Li, F. / Liu, Q. / Clarke, O.B. / Lam, S.M. / Shui, G.H. / Hendrickson, W.A. / Chen, Y.H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6iz3.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iz3.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 6iz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/6iz3 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/6iz3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6iyuC 6iyxC 6iyzC 6iz0C 6iz1C 6iz4C 6iz5SC 6iz6C 6izfC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35463.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: tmem38b-b / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q6GN30 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.56 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, KNO3 K-Citrate PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 21, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.78→47.85 Å / Num. obs: 24627 / % possible obs: 99.3 % / Redundancy: 37.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.039 / Rrim(I) all: 0.241 / Net I/σ(I): 9.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IZ5 Resolution: 3.791→47.845 Å / SU ML: 0.77 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.43
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 311.66 Å2 / Biso mean: 200.5016 Å2 / Biso min: 127.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.791→47.845 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
|