[English] 日本語
Yorodumi- PDB-5a51: The crystal structure of Arabidopsis thaliana CAR4 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a51 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of Arabidopsis thaliana CAR4 in complex with two calcium ions and phophatidyl serine | ||||||
Components | AT3G17980 | ||||||
Keywords | LIPID BINDING PROTEIN / CALCIUM BINDING PROTEIN / C2 DOMAIN | ||||||
Function / homology | Function and homology information positive regulation of response to salt stress / positive regulation of abscisic acid-activated signaling pathway / positive regulation of defense response to bacterium / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / phospholipid binding / defense response / lipid binding ...positive regulation of response to salt stress / positive regulation of abscisic acid-activated signaling pathway / positive regulation of defense response to bacterium / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / phospholipid binding / defense response / lipid binding / calcium ion binding / protein homodimerization activity / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å | ||||||
Authors | Diaz, M. / Albert, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Calcium-Dependent Oligomerization of Car Proteins at Cell Membrane Modulates Aba Signaling. Authors: Diaz, M. / Sanchez-Barrena, M.J. / Gonzalez-Rubio, J.M. / Rodriguez, L. / Fernandez, D. / Antoni, R. / Yunta, C. / Belda-Palazon, B. / Gonzalez-Guzman, M. / Peirats-Llobet, M. / Menendez, M. ...Authors: Diaz, M. / Sanchez-Barrena, M.J. / Gonzalez-Rubio, J.M. / Rodriguez, L. / Fernandez, D. / Antoni, R. / Yunta, C. / Belda-Palazon, B. / Gonzalez-Guzman, M. / Peirats-Llobet, M. / Menendez, M. / Boskovic, J. / Marquez, J.A. / Rodriguez, P.L. / Albert, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a51.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a51.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 5a51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a51_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5a51_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 5a51_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 5a51_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/5a51 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a51 | HTTPS FTP |
-Related structure data
Related structure data | 5a4xC 5a50C 5a52C 4v29S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9992, 0.03148, -0.02437), Vector: |
-Components
#1: Protein | Mass: 19926.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9LVH4 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SEP / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.01 % / Description: NONE |
---|---|
Crystal grow | Details: FROM 20 TO 25 % OF POLYETHYLENE GLYCOL 6K, 0.1M MES PH 6.0 TO 6.5 AND 0.1M LICL 5MM PSF |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.7 Å / Num. obs: 88958 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.6→1.72 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.7 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V29 Resolution: 1.602→46.787 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 22.15 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.278 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.602→46.787 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|