[English] 日本語
Yorodumi- PDB-4edj: Crystal structure of the GRASP55 GRASP Domain with a phosphomimet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4edj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the GRASP55 GRASP Domain with a phosphomimetic mutation (S189D) | ||||||
Components | Golgi reassembly-stacking protein 2 | ||||||
Keywords | MEMBRANE PROTEIN / PDZ domain / Golgi tethering | ||||||
Function / homology | Function and homology information establishment of protein localization to plasma membrane / organelle assembly / organelle organization / cis-Golgi network / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi organization / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation / Golgi membrane ...establishment of protein localization to plasma membrane / organelle assembly / organelle organization / cis-Golgi network / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi organization / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Truschel, S.T. / Zhang, M. / Bachert, C. / Macbeth, M.R. / Linstedt, A.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Allosteric Regulation of GRASP Protein-dependent Golgi Membrane Tethering by Mitotic Phosphorylation. Authors: Truschel, S.T. / Zhang, M. / Bachert, C. / Macbeth, M.R. / Linstedt, A.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4edj.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4edj.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 4edj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/4edj ftp://data.pdbj.org/pub/pdb/validation_reports/ed/4edj | HTTPS FTP |
---|
-Related structure data
Related structure data | 3rleS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22879.537 Da / Num. of mol.: 2 / Fragment: GRASP55 (UNP Residues 1-208) / Mutation: S189D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GORASP2, GOLPH6 / Plasmid: pRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H8Y8 #2: Chemical | ChemComp-K / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.2M ammonium acetate, 0.1M Tris pH 9.0, 0.1M immidazole, 30% PEG 4000, 10% PEG 20,000, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54148 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 29, 2010 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54148 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→58.9 Å / Num. all: 35319 / Num. obs: 34613 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rsym value: 0.087 / Net I/σ(I): 22.2 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RLE Resolution: 1.901→58.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.316 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.173 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 37.712 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→58.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
|