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Yorodumi- PDB-3pd4: Crystal structure of the editing domain of threonyl-tRNA syntheta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pd4 | ||||||
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Title | Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with glycyl-3'-aminoadenosine | ||||||
Components | Threonyl-tRNA synthetase | ||||||
Keywords | LIGASE / alpha/beta fold / deacylase / editing / aminoacyl-tRNA synthetase / translation | ||||||
Function / homology | Function and homology information threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Mechanistic insights into cognate substrate discrimination during proofreading in translation Authors: Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Deshmukh, M.V. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pd4.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pd4.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 3pd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/3pd4 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/3pd4 | HTTPS FTP |
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-Related structure data
Related structure data | 3pd2C 3pd3C 3pd5C 1y2qS 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
#1: Protein | Mass: 16738.312 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PAB1490, PYRAB13430, thrS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UZ14, threonine-tRNA ligase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | SEQUENCE OF THE PROTEIN USED IN THIS STUDY WAS THE FRAGMENT OF UNP RESIDUES 1-183 OF DATABASE ...SEQUENCE OF THE PROTEIN USED IN THIS STUDY WAS THE FRAGMENT OF UNP RESIDUES 1-183 OF DATABASE Q9UZ14 (SYT_PYRAB). BUT THE C-TERMINAL PROBABLY HAVE BEEN CLEAVED BEFORE CRYSTALLIZ | |
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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: 1.97 Å3/Da / Density % sol: 37.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, Bis-Tris, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 17, 2009 / Details: Osmic mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. all: 10812 / Num. obs: 10812 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.5 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y2Q Resolution: 2.4→24.85 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.683 / SU ML: 0.232 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 1.168 / ESU R Free: 0.346 / 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: 32.397 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.402→2.465 Å / Total num. of bins used: 20
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Xplor file |
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