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- PDB-1b7y: PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b7y | ||||||
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Title | PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE | ||||||
![]() | (PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)) x 2 | ||||||
![]() | LIGASE / ENZYME / TRNA SYNTHETASE / ALPHA/BETA HOMODIMER | ||||||
Function / homology | ![]() phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reshetnikova, L. / Moor, N. / Lavrik, O. / Vassylyev, D.G. | ||||||
![]() | ![]() Title: Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. Authors: Reshetnikova, L. / Moor, N. / Lavrik, O. / Vassylyev, D.G. #1: ![]() Title: The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Authors: Goldgur, Y. / Mosyak, L. / Reshetnikova, L. / Ankilova, V. / Lavrik, O. / Khodyreva, S. / Safro, M. #2: ![]() Title: Structure of Phenylalanyl-tRNA Synthetase from Thermus Thermophilus Authors: Mosyak, L. / Reshetnikova, L. / Goldgur, Y. / Delarue, M. / Safro, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.7 KB | Display | ![]() |
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PDB format | ![]() | 175.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b70C ![]() 1pysS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39309.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 86720.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-FYA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 313 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM ...Details: HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 75 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Details: Chernaya, M., (1987) J. Mol. Biol., 198, 555. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 81613 / Num. obs: 81613 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.2 / % possible all: 88.5 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 88.5 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PYS Resolution: 2.5→50 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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