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Yorodumi- PDB-3add: Crystal structure of O-phosphoseryl-tRNA kinase complexed with se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3add | ||||||
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Title | Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 3) | ||||||
Components |
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Keywords | TRANSFERASE/RNA / Protein-RNA complex / tRNA / ATP-binding / Kinase / Nucleotide-binding / Transferase / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information O-phosphoseryl-tRNASec kinase / L-seryl-tRNA(Sec) kinase activity / conversion of seryl-tRNAsec to selenocys-tRNAsec / tRNA wobble uridine modification / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) Methanopyrus kandleri (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Itoh, Y. / Chiba, S. / Sekine, S. / Yokoyama, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine Authors: Chiba, S. / Itoh, Y. / Sekine, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3add.cif.gz | 218.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3add.ent.gz | 168.2 KB | Display | PDB format |
PDBx/mmJSON format | 3add.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/3add ftp://data.pdbj.org/pub/pdb/validation_reports/ad/3add | HTTPS FTP |
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-Related structure data
Related structure data | 3adbSC 3adcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31196.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: MJ1538 / Plasmid: pCold II / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) References: UniProt: Q58933, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: RNA chain | Mass: 29714.688 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: tRNASec was prepared by in vitro transcription with T7 RNA polymerase. Source: (synth.) Methanopyrus kandleri (archaea) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RNA USES NON-SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 14.5% PEG 3350, 40mM sodium citrate-HCl (pH 5.2), 260mM ammonium tartrate, 5.0mM magnesium chloride, 1.0mM AMPPNP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 26, 2009 / Details: monochromator |
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: 2.4→50 Å / Num. all: 43686 / Num. obs: 39929 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.56 / Num. unique all: 4253 / Rsym value: 0.553 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ADB Resolution: 2.4→40.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1720323.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4913 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→40.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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