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- PDB-1jjc: Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jjc | ||||||
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Title | Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese | ||||||
![]() | (PHENYLALANYL-TRNA SYNTHETASE ...) x 2 | ||||||
![]() | LIGASE / Heterodimer / phenylalanyl-tRNA / Thermus thermophilus | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Safro, M.G. / Fishman, R. / Moor, N. / Ankilova, V. | ||||||
![]() | ![]() Title: Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese. Authors: Fishman, R. / Ankilova, V. / Moor, N. / Safro, M. #1: ![]() Title: Structure pf phenylalanyl-tRNA synthetase from Thermus thermophilus Authors: Mosyak, L. / Reshetnikova, L. / Goldgur, Y. / Delarue, M. / Safro, M. #2: ![]() Title: The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus complexed with cognate tRNA-Phe Authors: Goldgur, Y. / Mosyak, L. / Reshetnikova, L. / Ankilova, V. / Khodyreva, S. / Safro, M. #3: ![]() Title: Crystal Structures of phenylalnyl-tRNA synthetase complexed with phenylalanine and phenylalanyl-adenylate analogue Authors: Reshenikova, L. / Moor, N. / Lavrik, O. / Vassyliev, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227 KB | Display | ![]() |
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PDB format | ![]() | 177.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.2 KB | Display | ![]() |
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Full document | ![]() | 505.8 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pysS 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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Details | The second part of the molecule is generated by the two fold axis: y,x,-z' |
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Components
-PHENYLALANYL-TRNA SYNTHETASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 39309.199 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 86720.656 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 4 types, 292 molecules ![](data/chem/img/FA5.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FA5 / |
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#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.76 Å3/Da / Density % sol: 74.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: (NH4)2SO4, Imidazole-HCl, ATP, L-phenylalanine, MnSO4, pH 7.8, VAPOR DIFFUSION, HANGING DROP at 277K |
Crystal grow | *PLUS |
Components of the solutions | *PLUS Conc.: 27 %sat / Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD / Date: Feb 17, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 75189 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.8 |
Reflection | *PLUS Num. measured all: 405589 |
Reflection shell | *PLUS % possible obs: 81.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PYS Resolution: 2.6→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 45.2 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.003
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.216 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.2 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.37 / Rfactor Rwork: 0.31 |