[English] 日本語
![](img/lk-miru.gif)
- PDB-4rqf: human Seryl-tRNA synthetase dimer complexed with one molecule of ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4rqf | ||||||
---|---|---|---|---|---|---|---|
Title | human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec | ||||||
![]() |
| ||||||
![]() | LIGASE/RNA / aminoacyl-tRNA synthetase / classII aaRS / aminoacylation / serine / cytosol / LIGASE-RNA complex | ||||||
Function / homology | ![]() selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / mitochondrial seryl-tRNA aminoacylation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / selenocysteine incorporation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / mitochondrial seryl-tRNA aminoacylation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / selenocysteine incorporation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis / tRNA binding / molecular adaptor activity / cytoplasmic translation / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / extracellular exosome / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, W. / Wang, C. / Guo, Y. / Tian, Q. / Jia, Q. | ||||||
![]() | ![]() Title: SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis. Authors: Wang, C. / Guo, Y. / Tian, Q. / Jia, Q. / Gao, Y. / Zhang, Q. / Zhou, C. / Xie, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 232.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 179 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rqeC ![]() 3a3aS ![]() 4l87S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 28948.107 Da / Num. of mol.: 1 / Mutation: C2G, G70C / Source method: obtained synthetically / Details: in vitro synthesis / Source: (synth.) ![]() | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 59934.441 Da / Num. of mol.: 2 / Mutation: E447K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0., VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.503→50 Å / Num. all: 20009 / Num. obs: 19748 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 115.87 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 3.5→3.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.956 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4L87, 3A3A Resolution: 3.503→37.625 Å / SU ML: 0.47 / σ(F): 1.37 / Phase error: 34.14 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.503→37.625 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|