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Yorodumi- PDB-4jxx: Crystal structure of E coli E. coli glutaminyl-tRNA synthetase bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jxx | ||||||
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Title | Crystal structure of E coli E. coli glutaminyl-tRNA synthetase bound to tRNA(Gln)(CUG) and ATP from novel cryostabilization conditions | ||||||
Components |
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Keywords | ligase/rna / Rossmann fold / protein-RNA complex / transfer RNA / tRNA aminoacylation / tRNA(Gln) / ligase-rna complex | ||||||
Function / homology | Function and homology information glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Perona, J.J. / Rodriguez-Hernandez, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position. Authors: Rodriguez-Hernandez, A. / Spears, J.L. / Gaston, K.W. / Limbach, P.A. / Gamper, H. / Hou, Y.M. / Kaiser, R. / Agris, P.F. / Perona, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jxx.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jxx.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 4jxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jxx ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jxx | HTTPS FTP |
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-Related structure data
Related structure data | 4jxzC 4jyzC 1gtrS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 63434.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glnS, b0680, JW0666 / Production host: Escherichia coli (E. coli) / References: UniProt: P00962, glutamine-tRNA ligase |
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#2: RNA chain | Mass: 24060.287 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-ATP / |
#4: Chemical | ChemComp-SO4 / |
#5: 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: 3.54 Å3/Da / Density % sol: 65.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.4 w/v sodium citrate, 40 mM PIPES , 20 mM MgSO4, 20 mM b-mercaptoethanol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K PH range: 7.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 6, 2012 |
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41.1 Å / Num. all: 55577 / Num. obs: 55132 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1GTR Resolution: 2.3→41.1 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→41.1 Å
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Refine LS restraints |
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