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- PDB-7wrs: Crystal structure of the chicken isoleucyl-tRNA synthetase 1 (IAR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wrs | ||||||
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Title | Crystal structure of the chicken isoleucyl-tRNA synthetase 1 (IARS1) UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1) | ||||||
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![]() | TRANSLATION / Translation proteins / synthetase | ||||||
Function / homology | ![]() isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / glutamate-tRNA ligase activity / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / tRNA binding ...isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / glutamate-tRNA ligase activity / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / tRNA binding / 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 | ![]() | 211.7 KB | Display | ![]() |
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PDB format | ![]() | 133 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.5 KB | Display | ![]() |
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Full document | ![]() | 448.4 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wruC ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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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: Protein | Mass: 33130.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 0.84 M NaH2PO4, 1.76 M K2HPO4, and 0.1 M sodium acetate, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2782 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→77.8 Å / Num. obs: 39660 / % possible obs: 100 % / Redundancy: 622.9 % / Biso Wilson estimate: 50.62 Å2 / CC1/2: 0.995 / CC star: 0.999 / R split: 0.1438 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 3908 / R split: 0.649 |
Serial crystallography measurement | Collection time total: 12 hours / Collimation: Kirkpatrick-Baez mirrors / Pulse duration: 20 fsec. / Pulse photon energy: 9.7 keV |
Serial crystallography sample delivery | Description: fixed target / Method: fixed target |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4R3Z Resolution: 2.4→71.51 Å / SU ML: 0.3439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9538 / 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: 57.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→71.51 Å
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Refine LS restraints |
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LS refinement shell |
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