[English] 日本語
![](img/lk-miru.gif)
- PDB-6bq2: Crystal structure of Medicago truncatula Thermospermine Synthase ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6bq2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) | ||||||
![]() | Thermospermine synthase ACAULIS protein | ||||||
![]() | TRANSFERASE / polyamine biosynthesis / tetraamine / thermospermine / spermidine / aminopropyl transferase | ||||||
Function / homology | ![]() thermospermine synthase activity / spermidine synthase / spermidine synthase activity / polyamine biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sekula, B. / Dauter, Z. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases. Authors: Sekula, B. / Dauter, Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 248.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 198.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6bq3C ![]() 6bq4C ![]() 6bq5C ![]() 6bq6C ![]() 6bq7C ![]() 1inlS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 37279.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.17 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG3350, 0.1 M Magnesium Chloride and 0.1 M MES buffer; cryo 33% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 18, 2017 |
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: 1.68→46.81 Å / Num. obs: 62270 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.68→1.78 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.058 / Mean I/σ(I) obs: 2 / Num. unique obs: 9765 / % possible all: 98.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1INL Resolution: 1.68→46.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.253 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.105 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.349 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.68→46.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|