[English] 日本語
Yorodumi- PDB-2zr2: Crystal structure of seryl-tRNA synthetase from Pyrococcus horiko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zr2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with ATP | |||||||||
Components | Seryl-tRNA synthetase | |||||||||
Keywords | LIGASE / Coiled-coil / Homodimer / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Itoh, Y. / Sekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: Rna Biol. / Year: 2008 Title: Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. Authors: Itoh, Y. / Sekine, S. / Kuroishi, C. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zr2.cif.gz | 195.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zr2.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zr2 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zr2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2dq0SC 2zr3C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53342.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0710 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58441, serine-tRNA ligase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M ammonium sulfate, 0.1M magnesium acetate, 0.1M Hepes-NaOH pH 7.5, 2mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2005 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 37276 / Num. obs: 37201 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 101.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3657 / Rsym value: 0.612 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2dq0 Resolution: 2.8→48.52 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1691383.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.8289 Å2 / ksol: 0.344777 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|