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- PDB-2hl2: Crystal structure of the editing domain of threonyl-tRNA syntheta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hl2 | ||||||
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Title | Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate | ||||||
![]() | Threonyl-tRNA synthetase | ||||||
![]() | LIGASE / translation / editing / aminoacyl-tRNA synthetase / enzyme mechanism / enantioselectivity | ||||||
Function / homology | ![]() threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hussain, T. / Kruparani, S.P. / Pal, B. / Sankaranarayanan, R. | ||||||
![]() | ![]() Title: Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea Authors: Hussain, T. / Kruparani, S.P. / Pal, B. / Dock-Bregeon, A.C. / Dwivedi, S. / Shekar, M.R. / Sureshbabu, K. / Sankaranarayanan, R. #1: ![]() Title: A D-amino acid editing module coupled to the translational apparatus in archaea Authors: Dwivedi, S. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.4 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1017.2 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hkzC ![]() 2hl0C ![]() 2hl1C ![]() 1y2qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer |
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Components
#1: Protein | Mass: 16281.795 Da / Num. of mol.: 2 / Fragment: editing domain (residues 1-143) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2005 / 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: 2.6→25 Å / Num. all: 8487 / Num. obs: 8487 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.75 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.12 / Num. unique all: 724 / % possible all: 86.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Y2Q Resolution: 2.6→24.84 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 958280.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.1338 Å2 / ksol: 0.287978 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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