[English] 日本語
![](img/lk-miru.gif)
- PDB-3nen: Unliganded aspartyl-tRNA synthetase from thermococcus kodakarensis -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3nen | ||||||
---|---|---|---|---|---|---|---|
Title | Unliganded aspartyl-tRNA synthetase from thermococcus kodakarensis | ||||||
![]() | Aspartyl-tRNA synthetase | ||||||
![]() | LIGASE / aminoacyl-tRNA synthetase / Rossmann fold Ob fold / Aspartic acid / ATP-Mg / tRNA | ||||||
Function / homology | ![]() aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / magnesium ion binding / RNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmitt, E. / Moras, D. / Moulinier, L. | ||||||
![]() | ![]() Title: Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation Authors: Schmitt, E. / Moulinier, L. / Fujiwara, S. / Imanaka, T. / Thierry, J.C. / Moras, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 183.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 147.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 462.8 KB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b8aC ![]() 3nelC ![]() 3nemC ![]() 1aszS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 50979.414 Da / Num. of mol.: 2 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: 3.32 Å3/Da / Density % sol: 62.99 % |
---|---|
Crystal grow | Temperature: 297 K Details: peg and ethylen glycol, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 1996 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→37.268 Å / Num. obs: 48410 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.099 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ASZ Resolution: 2.4→37.27 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→37.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|