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Yorodumi- PDB-3akz: Crystal structure of Thermotoga maritima nondiscriminating glutam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3akz | ||||||
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Title | Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with tRNAGln and a glutamyl-AMP analog | ||||||
Components |
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Keywords | LIGASE/RNA / Protein-rna complex / LIGASE-RNA complex | ||||||
Function / homology | Function and homology information glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ito, T. / Yokoyama, S. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Authors: Ito, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3akz.cif.gz | 539.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3akz.ent.gz | 434.3 KB | Display | PDB format |
PDBx/mmJSON format | 3akz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3akz ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3akz | HTTPS FTP |
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-Related structure data
Related structure data | 3al0C 1n78S 3afhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: Protein | Mass: 57468.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: gltX2, TM_1875 / Plasmid: PET-28B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9X2I8, glutamate-tRNA ligase #2: RNA chain | Mass: 23858.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: T7 Transcription #3: Chemical | ChemComp-GSU / |
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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: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% 2-propanol, 0.2M magnesium chloride, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2009 / Details: mirrors |
Radiation | Monochromator: Rotated-inclined Si(111) double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.5 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 59965 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.109 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5139 / Rsym value: 0.47 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AFH, 1N78 Resolution: 2.9→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 Details: The crystal harbors twinning, and all refinement processes were performed with the twinning operator (h, -k, -l) with the twinning fraction of 0.5
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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