[English] 日本語
![](img/lk-miru.gif)
- PDB-2zt8: Crystal structure of human Glycyl-tRNA synthetase (GlyRS) in comp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2zt8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human Glycyl-tRNA synthetase (GlyRS) in complex with Gly-AMP analog | ||||||
![]() | Glycyl-tRNA synthetase | ||||||
![]() | LIGASE / AP4A / Glycine / ATP / Gly-AMP / tRNA / Aminoacyl-tRNA synthetase / ATP-binding / Charcot-Marie-Tooth disease / Disease mutation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis | ||||||
Function / homology | ![]() mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / protein dimerization activity / mitochondrial matrix / axon / mitochondrion / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, R.T. / Yang, X.L. / Schimmel, P. | ||||||
![]() | ![]() Title: Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis Authors: Guo, R.T. / Chong, Y.E. / Guo, M. / Yang, X.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 94.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 754.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 781.7 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zt5C ![]() 2zt6C ![]() 2zt7C ![]() 2zxfC ![]() 2pmeS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 78704.828 Da / Num. of mol.: 1 / Fragment: UNP residues 55-739 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-DRV / [( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.71 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25mM Tris-HCl, 150mM NaCl, 10mM MgCl2, 3.8-4.0M Sodium Formate, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: May 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. all: 16162 / Num. obs: 16000 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 3.35→50 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 7.9 / Num. unique all: 5508 / % possible all: 71.4 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PME Resolution: 3.35→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.86 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.71 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.35→50 Å
|