[English] 日本語
![](img/lk-miru.gif)
- PDB-8dae: Arabidopsis thaliana bifunctional dihydrofolate reductase-thymidy... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8dae | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Arabidopsis thaliana bifunctional dihydrofolate reductase-thymidylate synthase | |||||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase 1 | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() 10-formyltetrahydrofolate biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bond, C.S. / Haywood, J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Arabidopsis thaliana bifunctional dihydrofolate reductase-thymidylate synthase Authors: Bond, C.S. / Haywood, J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 149.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3i3rS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 60276.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q05762, ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.63 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 35% w/v poly(acrylic acid sodium salt)2100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→48.381 Å / Num. obs: 41582 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 3010 / CC1/2: 0.37 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3I3R Resolution: 2→48.381 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.074 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.15 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.554 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.381 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|