+Open data
-Basic information
Entry | Database: PDB / ID: 3hj7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TILS C-terminal domain | ||||||
Components | tRNA(Ile)-lysidine synthase | ||||||
Keywords | LIGASE / helix-turn-helix / pseudo-knot / ATP-binding / Nucleotide-binding / tRNA processing | ||||||
Function / homology | Function and homology information tRNAIle-lysidine synthase / ligase activity, forming carbon-nitrogen bonds / tRNA modification / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Nakanishi, K. / Bonnefond, L. / Kimura, S. / Suzuki, T. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Authors: Nakanishi, K. / Bonnefond, L. / Kimura, S. / Suzuki, T. / Ishitani, R. / Nureki, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hj7.cif.gz | 69 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hj7.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/3hj7 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/3hj7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3a2kSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16452.951 Da / Num. of mol.: 1 / Fragment: residues 332-464 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: GK0060, tilS / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus References: UniProt: Q5L3T3, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases | ||
---|---|---|---|
#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.44 % / Mosaicity: 0.357 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: LiSO4 1.5M, pH 8.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC-Q315 CCD / Detector: CCD / Date: Oct 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 14085 / Num. obs: 14085 / % possible obs: 96.8 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.071 / Χ2: 1.526 / Net I/σ(I): 66.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 0.247 / Num. unique all: 523 / Χ2: 0.57 / % possible all: 76.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A2K Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.745 / SU ML: 1.58 / SU R Cruickshank DPI: 0.262 / SU Rfree: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.203 / Phase error: 27.17 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 1.4 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.634 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.67 Å2 / Biso mean: 56.416 Å2 / Biso min: 31.47 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 32.6348 Å / Origin y: -30.3455 Å / Origin z: -14.9731 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain A |