[English] 日本語
Yorodumi- PDB-6yrl: Structure of the Chlamydomonas reinhardtii SAS-6 coiled-coil doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yrl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Chlamydomonas reinhardtii SAS-6 coiled-coil domain, C2 crystal form | |||||||||
Components | Centriole protein | |||||||||
Keywords | STRUCTURAL PROTEIN / centriole / centrosome / cartwheel / coiled coil / complex / alpha helical | |||||||||
Function / homology | Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / centriole / cell cycle / identical protein binding / cytoplasm / Centriole protein Function and homology information | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.343 Å | |||||||||
Authors | Kantsadi, A.L. / Vakonakis, I. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Structure / Year: 2022 Title: Structures of SAS-6 coiled coil hold implications for the polarity of the centriolar cartwheel. Authors: Kantsadi, A.L. / Hatzopoulos, G.N. / Gonczy, P. / Vakonakis, I. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6yrl.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6yrl.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 6yrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yrl_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6yrl_full_validation.pdf.gz | 425.2 KB | Display | |
Data in XML | 6yrl_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 6yrl_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yrl ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yrl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13057.345 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6, CHLRE_12g516950v5 / Plasmid: pFLOAT Details (production host): pET-30a derivative, N-terminal His6-tag Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CQL4 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.74 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.06 M divalent ions mixture, 0.1 M imidazole / MES buffer 20% v/v ethylene glycol 10% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.343→83.816 Å / Num. obs: 21732 / % possible obs: 88.1 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.343→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 526 / CC1/2: 0.895 / Rpim(I) all: 0.28 / Rrim(I) all: 0.481 / % possible all: 44.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.343→43.482 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 0.33 / Phase error: 37.11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.343→43.482 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|