[English] 日本語
![](img/lk-miru.gif)
- PDB-8enb: Crystal structure of LGR ligand alpha2/beta5 from C. elegans in c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8enb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of LGR ligand alpha2/beta5 from C. elegans in crystal form 2 | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() Hormone ligand-binding receptors / G alpha (s) signalling events / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gong, Z. / Hendrickson, W.A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Crystal structure of LGR ligand alpha2/beta5 from Caenorhabditis elegans with implications for the evolution of glycoprotein hormones Authors: Gong, Z. / Wang, W. / El Omari, K. / Lebedev, A.A. / Clarke, O.B. / Hendrickson, W.A. #1: ![]() Title: Combining AlphaFold and phenix.mr_rosetta for solving challenging crystal structures Authors: Wang, W. / Gong, Z. / Hendrickson, W.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8endC ![]() 8enfC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
|
-
Components
#1: Protein | ![]() Mass: 10565.464 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 11590.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.19 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 12% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→49.52 Å / Num. obs: 15726 / % possible obs: 86.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.63 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.3→2.47 Å / Num. unique obs: 787 / CC1/2: 0.264 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() 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: 41.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→49.52 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|