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- PDB-3al0: Crystal structure of the glutamine transamidosome from Thermotoga... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3al0 | ||||||
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Title | Crystal structure of the glutamine transamidosome from Thermotoga maritima in the glutamylation state. | ||||||
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![]() | LIGASE/RNA / Protein-rna complex / LIGASE-RNA complex | ||||||
Function / homology | ![]() glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / regulation of translational fidelity / tRNA binding ...glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / regulation of translational fidelity / tRNA binding / translation / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ito, T. / Yokoyama, S. | ||||||
![]() | ![]() Title: Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Authors: Ito, T. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 725.1 KB | Display | ![]() |
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PDB format | ![]() | 589.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 809.4 KB | Display | ![]() |
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Full document | ![]() | 937.5 KB | Display | |
Data in XML | ![]() | 70.5 KB | Display | |
Data in CIF | ![]() | 95.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Glutamyl-tRNA(Gln) amidotransferase subunit ... , 2 types, 2 molecules AC
#1: Protein | Mass: 52594.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X0Z9, glutaminyl-tRNA synthase (glutamine-hydrolysing) |
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#3: Protein | Mass: 69411.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The fused-protein of GatC and GluRS. THE FUSION PROTEIN COMPRISES RESIDUES 2-96 OF GATC, LINKER (GSGSGSGS) AND RESIDUES 1-487 OF GLURS Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: gatC, TM_0252, gltX2, TM_1875 / Plasmid: pET-Duet / Production host: ![]() ![]() References: UniProt: Q9WY94, UniProt: Q9X2I8, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor, glutamate-tRNA ligase |
-Protein / RNA chain , 2 types, 2 molecules BE
#2: Protein | Mass: 55514.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X100, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor |
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#4: RNA chain | Mass: 23858.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 Transcription / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GSU.gif)
![](data/chem/img/GSU.gif)
#5: Chemical | ChemComp-ZN / |
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#6: Chemical | ChemComp-GSU / |
-Details
Sequence details | THE CHAIN C IS THE FUSION PROTEIN. IT COMPRISES RESIDUES 2-96 OF GATC, LINKER (GSGSGSGS) AND ...THE CHAIN C IS THE FUSION PROTEIN. IT COMPRISES RESIDUES 2-96 OF GATC, LINKER (GSGSGSGS) AND RESIDUES 1-486 OF GLURS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 2.0M ammonium sulfate, 0.01M magnesium chloride, 0.05M sodium cacodylate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2009 / Details: mirrors |
Radiation | Monochromator: Rotated-inclined Si(111) double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. obs: 40894 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.118 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3028 / Rsym value: 0.396 / % possible all: 70 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.825 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.368→48.669 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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