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Yorodumi- PDB-2rkj: Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rkj | ||||||
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Title | Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA | ||||||
Components |
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Keywords | Ligase/RNA / RNA-protein complex / group I intron splicing factor / Aminoacyl-tRNA synthetase / ATP-binding / Ligase / Mitochondrion / mRNA processing / Nucleotide-binding / Protein biosynthesis / Transit peptide / Ligase-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Group I intron splicing / RNA folding / positive regulation of RNA splicing / mRNA processing / mitochondrial matrix / mitochondrion ...tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Group I intron splicing / RNA folding / positive regulation of RNA splicing / mRNA processing / mitochondrial matrix / mitochondrion / RNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus phage Twort (virus) Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.5 Å | ||||||
Authors | Paukstelis, P.J. / Chen, J.-H. / Chase, E. / Lambowitz, A.M. / Golden, B.L. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA. Authors: Paukstelis, P.J. / Chen, J.H. / Chase, E. / Lambowitz, A.M. / Golden, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rkj.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2rkj.ent.gz | 865.2 KB | Display | PDB format |
PDBx/mmJSON format | 2rkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rkj_validation.pdf.gz | 604.5 KB | Display | wwPDB validaton report |
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Full document | 2rkj_full_validation.pdf.gz | 950.2 KB | Display | |
Data in XML | 2rkj_validation.xml.gz | 166.6 KB | Display | |
Data in CIF | 2rkj_validation.cif.gz | 230.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/2rkj ftp://data.pdbj.org/pub/pdb/validation_reports/rk/2rkj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 79489.297 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage Twort (virus) / Genus: SPO1-like viruses / Gene: orf142-I2 / Genus (production host): SPO1-like viruses / Production host: Staphylococcus phage Twort (virus) #2: RNA chain | Mass: 1217.762 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: Protein | Mass: 44922.129 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: cyt-18 / Production host: Escherichia coli (E. coli) / References: UniProt: P12063, tyrosine-tRNA ligase |
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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: 4.92 Å3/Da / Density % sol: 75 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M cacodylate, 1.8 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97918 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2006 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→50 Å / Num. all: 79214 / Num. obs: 66194 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Χ2: 1.389 / Net I/σ(I): 11 |
Reflection shell | Resolution: 4.5→4.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.86 / Num. unique all: 3375 / Χ2: 1.037 / % possible all: 42.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1Y42, 1Y0Q Resolution: 4.5→47.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 7898242.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 202.284 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 211.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.5→47.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.5→4.78 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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