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- PDB-7wru: Crystal structure of the apo chicken glutamyl-tRNA synthetase 1 (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wru | ||||||
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Title | Crystal structure of the apo chicken glutamyl-tRNA synthetase 1 (EARS1) | ||||||
![]() | Glutamyl-tRNA synthetase | ||||||
![]() | TRANSLATION / Vertabrate / tRNA synthetase | ||||||
Function / homology | ![]() glutamate-tRNA ligase activity / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chung, S. / Cho, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1. Authors: Chung, S. / Kang, M.S. / Alimbetov, D.S. / Mun, G.I. / Yunn, N.O. / Kim, Y. / Kim, B.G. / Wie, M. / Lee, E.A. / Ra, J.S. / Oh, J.M. / Lee, D. / Lee, K. / Kim, J. / Han, S.H. / Kim, K.T. / ...Authors: Chung, S. / Kang, M.S. / Alimbetov, D.S. / Mun, G.I. / Yunn, N.O. / Kim, Y. / Kim, B.G. / Wie, M. / Lee, E.A. / Ra, J.S. / Oh, J.M. / Lee, D. / Lee, K. / Kim, J. / Han, S.H. / Kim, K.T. / Chung, W.K. / Nam, K.H. / Park, J. / Lee, B. / Kim, S. / Zhao, W. / Ryu, S.H. / Lee, Y.S. / Myung, K. / Cho, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.7 KB | Display | ![]() |
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PDB format | ![]() | 86.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.7 KB | Display | ![]() |
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Full document | ![]() | 444.4 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wrsC ![]() 4r3zS S: Starting model for refinement 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: 61159.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5ZJ86, proline-tRNA ligase, glutamate-tRNA ligase | ||||
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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: 2.76 Å3/Da / Density % sol: 55.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 85 mM HEPES (pH 7.5), 8.5% isopropanol, 15% glycerol, 40 mM NaF and 15% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0094 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.36 Å / Num. obs: 23252 / % possible obs: 98.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.66 Å2 / CC1/2: 0.976 / Rrim(I) all: 0.386 / Net I/σ(I): 8.11 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 2352 / CC1/2: 0.612 / Rrim(I) all: 2.885 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4R3Z Resolution: 2.5→45.36 Å / SU ML: 0.3663 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.6099 / 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: 54.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.36 Å
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Refine LS restraints |
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LS refinement shell |
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