[English] 日本語
![](img/lk-miru.gif)
- PDB-5uv1: Crystal Structure of (+)-Limonene Synthase Complexed with 2-Fluor... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5uv1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of (+)-Limonene Synthase Complexed with 2-Fluorogeranyl Diphosphate | ||||||
![]() | (+)-limonene synthase | ||||||
![]() | LYASE / Terpene synthase / enantiomer / terpene synthase fold / monoterpene / fluorinated analog | ||||||
Function / homology | ![]() (R)-limonene synthase / (R)-limonene synthase activity / diterpenoid biosynthetic process / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Prem Kumar, R. / Malik, K. / Oprian, D.D. | ||||||
![]() | ![]() Title: Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues. Authors: Kumar, R.P. / Morehouse, B.R. / Matos, J.O. / Malik, K. / Lin, H. / Krauss, I.J. / Oprian, D.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 125.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 94 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 726.7 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uv2C ![]() 5uv0S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | (+)- Mass: 70441.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-0FV / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.99 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG8000, 100 mM Tris pH 7.5, 350 mM sodium tartrate PH range: 7.5-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2016 / 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: 2.2→20 Å / Num. obs: 31630 / % possible obs: 98.7 % / Redundancy: 26.9 % / Biso Wilson estimate: 55.93 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5UV0 Resolution: 2.4→19.925 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.23
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.06 Å2 / Biso mean: 66.912 Å2 / Biso min: 34.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→19.925 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
|