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- PDB-1qtq: GLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA AND AN AMINO ACID ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qtq | ||||||
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Title | GLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA AND AN AMINO ACID ANALOG | ||||||
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![]() | LIGASE/RNA / TRNA SYNTHETASE / GLUTAMINE / TRNAGLN / E. COLI / COMPLEX / LIGASE-RNA COMPLEX | ||||||
Function / homology | ![]() glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rath, V.L. / Silvian, L.F. / Beijer, B. / Sproat, B.S. / Steitz, T.A. | ||||||
![]() | ![]() Title: How glutaminyl-tRNA synthetase selects glutamine. Authors: Rath, V.L. / Silvian, L.F. / Beijer, B. / Sproat, B.S. / Steitz, T.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 | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 125.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.8 KB | Display | ![]() |
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Full document | ![]() | 819.5 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 36.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gtrS 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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Unit cell |
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Components
#1: RNA chain | Mass: 24060.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 63434.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-QSI / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0 M AMMONIUM SULFATE, 20 MM MGSO4, 80 MM PIPES, PH 7.0, 1 MM QSI, AND 1:1 MOLAR RATIO OF TRNA TO PROTEIN AT 17 DEGREES C BY THE HANGING DROP METHOD., vapor diffusion - hanging drop, temperature 290.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / PH range low: 7.2 / PH range high: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995 / Details: PT COATED SI MIRROR |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.25→28 Å / Num. obs: 51376 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 1 % / Rmerge(I) obs: 0.534 / % possible all: 67.7 |
Reflection | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 28 Å / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 34.5 Å2 |
Reflection shell | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 2.3 Å / % possible obs: 67.7 % / Redundancy: 1 % / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GTR Resolution: 2.25→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1087461.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED RESIDUES 1 - 7, 443 - 453, AND 548 - 553 OF THE PROTEIN AND NUCLEOTIDE 901 OF THE TRNA ARE DISORDERED IN THE CRYSTAL STRUCTURE.
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Displacement parameters | Biso mean: 49.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.461 |