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- PDB-4pbt: Crystal structure of the M. jannaschii G2 tRNA synthetase variant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pbt | ||||||
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Title | Crystal structure of the M. jannaschii G2 tRNA synthetase variant bound to 4-trans-cyclooctene-amidopheylalanine (Tco-amF) | ||||||
![]() | Tyrosine--tRNA ligase | ||||||
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Function / homology | ![]() tyrosyl-tRNA aminoacylation / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cooley, R.B. / Karplus, P.A. / Mehl, R.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Gleaning Unexpected Fruits from Hard-Won Synthetases: Probing Principles of Permissivity in Non-canonical Amino Acid-tRNA Synthetases. Authors: Cooley, R.B. / Karplus, P.A. / Mehl, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.2 KB | Display | ![]() |
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PDB format | ![]() | 117.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pbrC ![]() 4pbsC ![]() 2zp1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 36113.906 Da / Num. of mol.: 1 / Mutation: Y32G, L65E, F108W, Q109M, D158S, L162K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: tyrS, MJ0389 / Production host: ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-P4G / ![]() |
#3: Chemical | ChemComp-GOL / ![]() |
#4: Chemical | ChemComp-2LQ / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20-22% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris PH range: 7.8-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→71.9 Å / Num. obs: 30390 / % possible obs: 100 % / Redundancy: 24.5 % / Net I/σ(I): 11.6 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2ZP1 Resolution: 1.9→71.9 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→71.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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