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Yorodumi- PDB-2du4: Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2du4 | ||||||
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Title | Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with tRNACys | ||||||
Components |
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Keywords | LIGASE/RNA / alpha4 tetramer / LIGASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information O-phospho-L-serine-tRNA ligase / phosphoserine-tRNA(Cys) ligase activity / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fukunaga, R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Authors: Fukunaga, R. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2du4.cif.gz | 241.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2du4.ent.gz | 190 KB | Display | PDB format |
PDBx/mmJSON format | 2du4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2du4_validation.pdf.gz | 473.8 KB | Display | wwPDB validaton report |
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Full document | 2du4_full_validation.pdf.gz | 537.6 KB | Display | |
Data in XML | 2du4_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 2du4_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/2du4 ftp://data.pdbj.org/pub/pdb/validation_reports/du/2du4 | HTTPS FTP |
-Related structure data
Related structure data | 2du3SC 2du5C 2du6C 2du7C 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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Details | The biological assembly is a tetramer of O-phosphoseryl-tRNA synthetase with two bound tRNACys molecules generated from the dimer O-phosphoseryl-tRNA synthetase with one bound tRNACys molecule in the asymmetric unit by the operations: y, x, -z |
-Components
#1: RNA chain | Mass: 22932.605 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Protein | Mass: 61265.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) References: UniProt: O30126, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds #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: 3.31 Å3/Da / Density % sol: 62.86 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 8% PEG 6000, 1.2M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2006 |
Radiation | 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: 47885 / Num. obs: 47199 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.1 Å2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DU3 Resolution: 2.8→49.01 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2997395.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.4875 Å2 / ksol: 0.332427 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→49.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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