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Yorodumi- PDB-2zuf: Crystal structure of Pyrococcus horikoshii arginyl-tRNA synthetas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zuf | ||||||
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Title | Crystal structure of Pyrococcus horikoshii arginyl-tRNA synthetase complexed with tRNA(Arg) | ||||||
Components |
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Keywords | Ligase/RNA / RRS/tRNA(Arg) / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Ligase / Nucleotide-binding / Protein biosynthesis / Ligase-RNA COMPLEX | ||||||
Function / homology | Function and homology information arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Konno, M. / Sumida, T. / Uchikawa, E. / Mori, Y. / Yanagisawa, T. / Sekine, S. / Yokoyama, S. | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP) Authors: Konno, M. / Sumida, T. / Uchikawa, E. / Mori, Y. / Yanagisawa, T. / 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 | 2zuf.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zuf.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zuf ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zuf | HTTPS FTP |
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-Related structure data
Related structure data | 2zueSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 72444.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: argS, PH1478 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59147, arginine-tRNA ligase |
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#2: RNA chain | Mass: 25161.041 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This tRNA occurs from Pyrococcus horikoshii, in vitro transcription Source: (synth.) synthetic construct (others) / References: GenBank: 14589963 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.33 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG 4000, 0.2M ammonium sulfate, 5mM magnesium chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 24, 2004 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 42799 / Num. obs: 38821 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.5 / % possible all: 79.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2ZUE Resolution: 2.3→39.65 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.44 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→39.65 Å
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Refine LS restraints |
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LS refinement shell |
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