[English] 日本語
Yorodumi- PDB-8ia1: plastidial glycerol-3-phosphate acyltransferases (GPAT) from the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ia1 | ||||||
---|---|---|---|---|---|---|---|
Title | plastidial glycerol-3-phosphate acyltransferases (GPAT) from the green alga Myrmecia incisa | ||||||
Components | Glycerol-3-phosphate acyltransferase, chloroplastic | ||||||
Keywords | TRANSFERASE / plastidial glycerol-3-phosphate acyltransferases | ||||||
Function / homology | Function and homology information glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / : / CDP-diacylglycerol biosynthetic process / chloroplast stroma Similarity search - Function | ||||||
Biological species | Lobosphaera incisa (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Song, X. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Unique recognition of the microalgal plastidial glycerol-3-phosphate acyltransferase for acyl-ACP Authors: Song, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ia1.cif.gz | 275.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ia1.ent.gz | 180.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ia1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ia1_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ia1_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 8ia1_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 8ia1_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/8ia1 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/8ia1 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41651.180 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lobosphaera incisa (plant) / Gene: GPAT / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B5EHP8 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2M (NH4)2SO4, 0.1M Tris-HCl pH 8.5, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.0001 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→37.32 Å / Num. obs: 50682 / % possible obs: 89.19 % / Redundancy: 2.2 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 0.99 / Net I/av σ(I): 16.1 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.31→2.38 Å / Mean I/σ(I) obs: 2.61 / Num. unique obs: 2902 / CC1/2: 0.76 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→37.32 Å / SU ML: 0.2843 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.9081 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→37.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|