[English] 日本語
![](img/lk-miru.gif)
- PDB-3mf1: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3mf1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of class II aaRS homologue (Bll0957) complexed with an analogue of glycyl adenylate | ||||||
![]() | Bll0957 protein | ||||||
![]() | LIGASE / aminoacyl-tRNA synthetase / seryl-tRNA synthetase / zinc ion / amino acid:[carrier protein] ligase / Bll0957 | ||||||
Function / homology | ![]() : / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Weygand-Durasevic, I. / Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. | ||||||
![]() | ![]() Title: Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis Authors: Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. / Weygand-Durasevic, I. #1: ![]() Title: Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition Authors: Bilokapic, S. / Maier, T. / Ahel, D. / Gruic-Sovulj, I. / Soll, D. / Weygand-Durasevic, I. / Ban, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38159.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.68 % |
---|---|
Crystal grow | Temperature: 291 K / Method: hanging drop / pH: 4.6 Details: PEG 4000, gycerol, pH 4.6, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Apr 21, 2009 |
Radiation | Monochromator: Nova optical assembly incorporating graded multilayer optics Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20.82 Å / Num. all: 34009 / Num. obs: 33974 / % possible obs: 99.62 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.04 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.7372 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 10.08 % / Rmerge(I) obs: 0.55 / Num. measured all: 48773 / Num. unique all: 4839 / % possible all: 99.39 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.67 Å2 / Biso mean: 27.438 Å2 / Biso min: 4.55 Å2
| ||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.256 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20.41 Å
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.27 Å / Total num. of bins used: 17
|