[English] 日本語
![](img/lk-miru.gif)
- PDB-6f87: Crystal structure of P. abyssi Sua5 complexed with L-threonine and PPi -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6f87 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of P. abyssi Sua5 complexed with L-threonine and PPi | ||||||
![]() | Threonylcarbamoyl-AMP synthase | ||||||
![]() | TRANSFERASE / Nucleotidyltransferase / tRNA modification / threonylcarbamoylation | ||||||
Function / homology | ![]() L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / regulation of translational fidelity / double-stranded RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pichard-Kostuch, A. / Zhang, W. / Liger, D. / Daugeron, M.C. / Letoquart, J. / Li de la Sierra-Gallay, I. / Forterre, P. / Collinet, B. / van Tilbeurgh, H. / Basta, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t6A tRNA modification. Authors: Pichard-Kostuch, A. / Zhang, W. / Liger, D. / Daugeron, M.C. / Letoquart, J. / Li de la Sierra-Gallay, I. / Forterre, P. / Collinet, B. / van Tilbeurgh, H. / Basta, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 269.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 220.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 496.7 KB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 66.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f89C ![]() 6f8yC ![]() 2eqaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
3 | ![]()
| |||||||||
4 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 38197.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: GE5 / Orsay / Gene: sua5, PYRAB15960, PAB1302 / Production host: ![]() ![]() References: UniProt: Q9UYB2, L-threonylcarbamoyladenylate synthase #2: Chemical | ChemComp-POP / #3: Chemical | ChemComp-THR / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.53 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate / PH range: 8.5 - 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→49.03 Å / Num. obs: 64452 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rrim(I) all: 0.071 / Net I/σ(I): 14.14 |
Reflection shell | Resolution: 2.62→2.78 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 10212 / Rrim(I) all: 0.69 / % possible all: 97.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2EQA Resolution: 2.62→49.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.58 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 236.33 Å2 / Biso mean: 66.881 Å2 / Biso min: 35.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→49.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.617→2.685 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|