[English] 日本語
![](img/lk-miru.gif)
- PDB-8d3z: Crystal structure of GalS1 in complex with Manganese from Populus... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8d3z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GalS1 in complex with Manganese from Populus trichocarpas | ||||||
![]() | Galactan synthase | ||||||
![]() | TRANSFERASE / glycosyltransferase galactan synthase | ||||||
Function / homology | Glycosyltransferase family 92 / Glycosyltransferase family 92 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / membrane / : / Glycosyltransferase family 92 protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pereira, J.H. / Prabhakar, P.K. / Urbanowicz, B.R. / Adams, P.D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural and biochemical insight into a modular beta-1,4-galactan synthase in plants. Authors: Prabhakar, P.K. / Pereira, J.H. / Taujale, R. / Shao, W. / Bharadwaj, V.S. / Chapla, D. / Yang, J.Y. / Bomble, Y.J. / Moremen, K.W. / Kannan, N. / Hammel, M. / Adams, P.D. / Scheller, H.V. / Urbanowicz, B.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 369.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 293.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d3tSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48845.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A2K2AMS7, Transferases; Glycosyltransferases; Hexosyltransferases |
---|
-Sugars , 3 types, 12 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 2 types, 39 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0 10 % PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→49.07 Å / Num. obs: 79592 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 68.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.56→2.65 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 7908 / CC1/2: 0.755 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8D3T Resolution: 2.56→49.07 Å / SU ML: 0.4108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2787 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: 107.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→49.07 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|