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Yorodumi- PDB-1y2q: Crystal structure of the editing domain of threonyl-tRNA syntheta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y2q | ||||||
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Title | Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi | ||||||
Components | Threonyl-tRNA synthetase | ||||||
Keywords | LIGASE / beta-alpha-beta fold / editing domain / tRNA-synthetase | ||||||
Function / homology | Function and homology information threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.95 Å | ||||||
Authors | Dwivedi, S. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: A D-amino acid editing module coupled to the translational apparatus in archaea Authors: Dwivedi, S. / Kruparani, S.P. / Sankaranarayanan, R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria Authors: Dwivedi, S. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y2q.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y2q.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 1y2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/1y2q ftp://data.pdbj.org/pub/pdb/validation_reports/y2/1y2q | HTTPS FTP |
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-Related structure data
Related structure data | 1y2r |
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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: 16281.795 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: thrS / Plasmid: pET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UZ14, threonine-tRNA ligase |
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#2: 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: 1.7 Å3/Da / Density % sol: 27.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2004 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. all: 10459 / Num. obs: 10459 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.25 / Num. unique all: 928 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.785 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.198 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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