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Yorodumi- PDB-4j15: Crystal structure of human cytosolic aspartyl-tRNA synthetase, a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j15 | ||||||
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Title | Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex | ||||||
Components | Aspartate--tRNA ligase, cytoplasmic | ||||||
Keywords | LIGASE / aspartyl-tRNA synthetase / tRNA | ||||||
Function / homology | Function and homology information aminoacylase activity / aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / protein-containing complex assembly / translation / synapse ...aminoacylase activity / aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / protein-containing complex assembly / translation / synapse / RNA binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Kim, K.R. / Park, S.H. / Kim, H.S. / Kim, B.-G. / Kim, D.G. / Rhee, K.H. / Park, M.S. / Kim, H.-J. / Kim, S. / Han, B.W. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex Authors: Kim, K.R. / Park, S.H. / Kim, H.S. / Rhee, K.H. / Kim, B.-G. / Kim, D.G. / Park, M.S. / Kim, H.-J. / Kim, S. / Han, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j15.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j15.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 4j15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/4j15 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/4j15 | HTTPS FTP |
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-Related structure data
Related structure data | 1aszS S: Starting model for refinement |
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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: 59384.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DARS / Production host: Escherichia coli (E. coli) / References: UniProt: P14868, aspartate-tRNA ligase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG3350, 8% tacsimate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 48428 / % possible obs: 99.3 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 |
Reflection shell | Resolution: 2.25→2.29 Å / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ASZ Resolution: 2.24→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.905 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.184 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.242→2.3 Å / Total num. of bins used: 20
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