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Yorodumi- PDB-4s03: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s03 | ||||||
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Title | Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A mutant | ||||||
Components | Threonine--tRNA ligase | ||||||
Keywords | LIGASE / beta-alpha-beta fold / editing domain / tRNA-synthetase / Biphenylalanine and unnatural amino acid / threonine-tRNA ligase | ||||||
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 GE5 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Pearson, A.D. / Mills, J.H. / Song, Y. / Nasertorabi, F. / Han, G.W. / Baker, D. / Stevens, R.C. / Schultz, P.G. | ||||||
Citation | Journal: Science / Year: 2015 Title: Transition states. Trapping a transition state in a computationally designed protein bottle. Authors: Pearson, A.D. / Mills, J.H. / Song, Y. / Nasertorabi, F. / Han, G.W. / Baker, D. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s03.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s03.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 4s03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/4s03 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/4s03 | HTTPS FTP |
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-Related structure data
Related structure data | 4s02C 4s0iC 4s0jC 4s0kC 4s0lC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17343.961 Da / Num. of mol.: 1 / Fragment: threonyl-tRNA synthetase / Mutation: I11BIF, Y79I, F123A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: PAB1490, PYRAB13430, thrS / Plasmid: pET-22b and pULTRA / Production host: Escherichia coli (E. coli) / 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: 2.73 Å3/Da / Density % sol: 54.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.75 Details: 0.1 M sodium citrate, 15% PEG 6000, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 12224 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.3 / Num. unique all: 930 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1y2q Resolution: 2.05→31.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.642 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.029 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.504 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→31.58 Å
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Refine LS restraints |
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