[English] 日本語
![](img/lk-miru.gif)
- PDB-5ilk: Tobacco 5-epi-aristolochene synthase with partial density from MO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ilk | ||||||
---|---|---|---|---|---|---|---|
Title | Tobacco 5-epi-aristolochene synthase with partial density from MOPSO or BIS-TRIS buffer molecule in the active site | ||||||
![]() | 5-epi-aristolochene synthase | ||||||
![]() | LYASE / terpene synthase / TEAS / MOPSO / BIS-TRIS | ||||||
Function / homology | ![]() 5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / sesquiterpene biosynthetic process / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P. | ||||||
![]() | ![]() Title: Small-molecule buffer components can directly affect terpene-synthase activity by interacting with the substrate-binding site of the enzyme Authors: Koo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 235.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 189.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5il3C ![]() 5il8C ![]() 5ildC ![]() 5ilhC ![]() 5iliC ![]() 5iljC ![]() 5ilyC ![]() 5ilzC ![]() 5im1SC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 63201.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.73 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Reservoir: 100 mM MOPSO, pH 7, 300 mM Mg Acetate, 13% PEG 8000 Soaked in 50 mM MOPSO (pH 7), 10 mM BIS-TRIS (pH 6.5) 110 mM Mg Acetate, 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50.77 Å / Num. obs: 35665 / % possible obs: 83.97 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09516 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.35→2.434 Å / Redundancy: 3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.52 / % possible all: 64.51 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5IM1 Resolution: 2.35→50.767 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.31
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→50.767 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|