[English] 日本語
![](img/lk-miru.gif)
- PDB-1q11: Crystal structure of an active fragment of human tyrosyl-tRNA syn... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1q11 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an active fragment of human tyrosyl-tRNA synthetase with tyrosinol | ||||||
![]() | Tyrosyl-tRNA synthetase | ||||||
![]() | LIGASE / Rossmann fold domain containing the active site / anticodon recognition domain / substrate analog tyrosinol co-crystalized | ||||||
Function / homology | ![]() methionyl glutamyl tRNA synthetase complex / interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body ...methionyl glutamyl tRNA synthetase complex / interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / RNA binding / extracellular space / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, X.-L. / Schimmel, P. / Ribas de Pouplana, L. | ||||||
![]() | ![]() Title: Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains Authors: Yang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Schimmel, P. / Ribas De Pouplana, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 473.8 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r6tC ![]() 1n3lS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | asymmetric unit contains a monomer of the biologically dimer |
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 353 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/TYE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/TYE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / | ||
---|---|---|---|
#3: Chemical | ChemComp-K / | ||
#4: Chemical | ChemComp-TYE / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: (NH4)2SO4, NAH2PO4, K2HPO4, ACETONE, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 58862 / Num. obs: 53993 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.301 / % possible all: 64.5 |
Reflection | *PLUS Num. obs: 55381 / % possible obs: 93.8 % / Redundancy: 6.7 % |
Reflection shell | *PLUS % possible obs: 64.5 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1N3L, mini TyrRS alone Resolution: 1.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |