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Open data
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Basic information
Entry | Database: PDB / ID: 7c5c | ||||||
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Title | Crystal structure of SeFRS | ||||||
![]() | Tyrosine--tRNA ligase | ||||||
![]() | LIGASE / AMINOACYL-TRNA SYNTHETASE | ||||||
Function / homology | ![]() tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, J.P. / Wang, J.Y. / Zhu, Z.L. / He, Q.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CRYSTAL STRUCTURE OF SeFRS Authors: Sun, J.P. / Wang, J.Y. / Zhu, Z.L. / He, Q.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.9 KB | Display | ![]() |
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PDB format | ![]() | 112.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.6 KB | Display | ![]() |
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Full document | ![]() | 432.6 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hjrS 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36022.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: tyrS, MJ0389 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% Polyethylene glycol (PEG) 3350, 100mM Bis-Tris(pH5.5), 200mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→44.73 Å / Num. obs: 35051 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.034 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.72→1.75 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1201 / CC1/2: 0.926 / Rrim(I) all: 0.387 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HJR Resolution: 1.72→44.73 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9605 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→44.73 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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