[English] 日本語
![](img/lk-miru.gif)
- PDB-1ggm: GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH G... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ggm | ||||||
---|---|---|---|---|---|---|---|
Title | GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE | ||||||
![]() | Glycine--tRNA ligase | ||||||
![]() | LIGASE / AMINOACYL-TRNA SYNTHASE / LIGASE(SYNTHETASE) | ||||||
Function / homology | ![]() glycine-tRNA ligase complex / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / glycine binding / protein dimerization activity / magnesium ion binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Arnez, J.G. / Moras, D. | ||||||
![]() | ![]() Title: Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine. Authors: Arnez, J.G. / Dock-Bregeon, A.C. / Moras, D. #1: ![]() Title: Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. Authors: Logan, D.T. / Mazauric, M.H. / Kern, D. / Moras, D. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and initial crystallographic data. Authors: Logan, D.T. / Cura, V. / Touzel, J.P. / Kern, D. / Moras, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 225.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 180.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 912.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 971.1 KB | Display | |
Data in XML | ![]() | 39.4 KB | Display | |
Data in CIF | ![]() | 53.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.637077, -0.707897, 0.304983), Vector: |
-
Components
#1: Protein | Mass: 51144.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: glyQS, glyS, TTHA0543 / Plasmid: PGRS / Gene (production host): GLYS / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | A P56206 96 - 158 GAP IN PDB ENTRY B P56206 96 - 158 GAP IN PDB ENTRY | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 297 K / pH: 8 / Details: pH 8.0, temperature 297K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 272 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 1996 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→15 Å / Num. all: 20549 / Num. obs: 20549 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.073 / Rsym value: 7.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 3.4→9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: FINAL RMS COORD. SHIFT 0.015 ANGSTROMS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.4→3.55 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|