+Open data
-Basic information
Entry | Database: PDB / ID: 6f8y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of P. abyssi Sua5 complexed with L-threonine | ||||||
Components | Threonylcarbamoyl-AMP synthase | ||||||
Keywords | TRANSFERASE / Nucleotidyltransferase / tRNA modification / threonylcarbamoylation | ||||||
Function / homology | Function and homology information L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / double-stranded RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
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. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: RNA / Year: 2018 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f8y.cif.gz | 267.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f8y.ent.gz | 217.4 KB | Display | PDB format |
PDBx/mmJSON format | 6f8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/6f8y ftp://data.pdbj.org/pub/pdb/validation_reports/f8/6f8y | HTTPS FTP |
---|
-Related structure data
Related structure data | 6f87C 6f89C 2eqaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38197.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Strain: GE5 / Orsay / Gene: sua5, PYRAB15960, PAB1302 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UYB2, L-threonylcarbamoyladenylate synthase #2: Chemical | ChemComp-THR / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % |
---|---|
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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
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: 2.86→48.781 Å / Num. obs: 49934 / % possible obs: 99.33 % / Redundancy: 3.76 % / Rrim(I) all: 0.09 / Net I/σ(I): 10.66 |
Reflection shell | Resolution: 2.86→3.03 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EQA Resolution: 2.86→48.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.818 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.806 / ESU R Free: 0.347 / 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: 188.95 Å2 / Biso mean: 79.276 Å2 / Biso min: 27.81 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.86→48.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.856→2.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|