[English] 日本語
Yorodumi- PDB-2xtz: Crystal structure of the G alpha protein AtGPA1 from Arabidopsis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xtz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the G alpha protein AtGPA1 from Arabidopsis thaliana | ||||||
Components | GUANINE NUCLEOTIDE-BINDING PROTEIN ALPHA-1 SUBUNIT | ||||||
Keywords | HYDROLASE / G-PROTEIN SIGNALING / SELF-ACTIVATION / RAS-LIKE DOMAIN | ||||||
Function / homology | Function and homology information thylakoid membrane organization / response to low fluence blue light stimulus by blue low-fluence system / blue light signaling pathway / positive regulation of abscisic acid-activated signaling pathway / gibberellic acid mediated signaling pathway / regulation of stomatal closure / response to pheromone / seed germination / tyrosine biosynthetic process / regulation of stomatal movement ...thylakoid membrane organization / response to low fluence blue light stimulus by blue low-fluence system / blue light signaling pathway / positive regulation of abscisic acid-activated signaling pathway / gibberellic acid mediated signaling pathway / regulation of stomatal closure / response to pheromone / seed germination / tyrosine biosynthetic process / regulation of stomatal movement / cell death / GTPase inhibitor activity / L-phenylalanine biosynthetic process / plasmodesma / channel regulator activity / abscisic acid-activated signaling pathway / response to glucose / reactive oxygen species metabolic process / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / peroxisome / heterotrimeric G-protein complex / GTPase binding / regulation of cell population proliferation / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / endoplasmic reticulum membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Jones, J.C. / Duffy, J.W. / Machius, M. / Temple, B.R.S. / Dohlman, H.G. / Jones, A.M. | ||||||
Citation | Journal: Sci.Signal. / Year: 2011 Title: The Crystal Structure of a Self-Activating G Protein Alpha Subunit Reveals its Distinct Mechanism of Signal Initiation Authors: Jones, J.C. / Duffy, J.W. / Machius, M. / Temple, B.R.S. / Dohlman, H.G. / Jones, A.M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Gtpase Acceleration as the Rate-Limiting Step in Arabidopsis G Protein-Coupled Sugar Signaling. Authors: Johnston, C.A. / Taylor, J.P. / Gao, Y. / Kimple, A.J. / Grigston, J.C. / Chen, J. / Siderovski, D.P. / Jones, A.M. / Willard, F.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xtz.cif.gz | 410.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xtz.ent.gz | 336.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xtz ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xtz | HTTPS FTP |
---|
-Related structure data
Related structure data | 1fqjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 41075.090 Da / Num. of mol.: 3 / Fragment: RESIDUES 37-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PPROEX-HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS (RIPL) / References: UniProt: P18064, EC: 3.6.5.1 |
---|
-Non-polymers , 5 types, 264 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | THE 36 N-TERMINAL RESIDUES OF THE FULL-LENGTH PROTEIN WERE REMOVED FOR CRYSTALLIZATION PURPOSES. ...THE 36 N-TERMINAL RESIDUES OF THE FULL-LENGTH PROTEIN WERE REMOVED FOR CRYSTALLIZ |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53.3 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: CRYSTALS OF ATGPA1 WERE GROWN AT 4 DEGREES CELSIUS USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. DROPS CONTAINED 1.5 UL OF PROTEIN SOLUTION (20 MG/ML ATGPA1 IN 25 MM TRIS-HCL, PH 7.4, 5% ...Details: CRYSTALS OF ATGPA1 WERE GROWN AT 4 DEGREES CELSIUS USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. DROPS CONTAINED 1.5 UL OF PROTEIN SOLUTION (20 MG/ML ATGPA1 IN 25 MM TRIS-HCL, PH 7.4, 5% (V/V) GLYCEROL, 150 MM SODIUM CHLORIDE, 1 MM DTT, 500 UL GTP-GAMMA-S) AND WERE EQUILIBRATED AGAINST 1.5 UL OF 0.3 M MAGNESIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH 6.0, 21% (W/V) PEG 8000. INITIALLY OBTAINED CRYSTALS WERE USED FOR MACROSEEDING. CRYSTALS REACHED THEIR FINAL ROD-SHAPE FORM WITHIN 14 DAYS AFTER MACROSEEDING AND WERE CRYOPROTECTED IN THE MOTHER LIQUOR WITH 8% (V/V) GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH MX300 / Detector: CCD / Date: Nov 16, 2009 / Details: CUSTOM |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→44.6 Å / Num. obs: 55808 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.34→2.36 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FQJ Resolution: 2.34→96.03 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.851 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.512 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→96.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|