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- PDB-9sfb: Structure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9sfb | ||||||
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Title | Structure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to a tRNA(Tyr)(GUA) transcript, the sulphamoyl analogue of tyrosyl-adenylate and pyrophosphate. | ||||||
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![]() | RNA BINDING PROTEIN / aminoacyl-tRNA synthetase / ligase / tRNA | ||||||
Function / homology | ![]() tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cusack, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. Authors: Yaremchuk, A. / Kriklivyi, I. / Tukalo, M. / Cusack, 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 | ![]() | 151.4 KB | Display | ![]() |
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PDB format | ![]() | 109 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.5 KB | Display | ![]() |
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Full document | ![]() | 750.4 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h3eC ![]() 1h3fC ![]() 9sdfC ![]() 9sfqC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48786.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: RNA chain | Mass: 27681.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G9 replaced by U9 / Source: (synth.) ![]() ![]() | ||||||
#3: Chemical | ChemComp-PPV / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-YSA / | Has ligand of interest | Y | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.99 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: Don't know |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→23 Å / Num. obs: 29086 / % possible obs: 97.06 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.7→2.77 Å / Rmerge(I) obs: 0.352 / Num. unique obs: 5814 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.246 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→23 Å
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Refine LS restraints |
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LS refinement shell |
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