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- PDB-7rou: Structure of human tyrosyl tRNA synthetase in complex with ML901-Tyr -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rou | |||||||||
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Title | Structure of human tyrosyl tRNA synthetase in complex with ML901-Tyr | |||||||||
![]() | Tyrosine--tRNA ligase, cytoplasmic | |||||||||
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Function / homology | ![]() methionyl glutamyl tRNA synthetase complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Metcalfe, R.D. / Xie, S.C. / Morton, C.J. / Tilley, L. / Griffin, M.D.W. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy. Authors: Xie, S.C. / Metcalfe, R.D. / Dunn, E. / Morton, C.J. / Huang, S.C. / Puhalovich, T. / Du, Y. / Wittlin, S. / Nie, S. / Luth, M.R. / Ma, L. / Kim, M.S. / Pasaje, C.F.A. / Kumpornsin, K. / ...Authors: Xie, S.C. / Metcalfe, R.D. / Dunn, E. / Morton, C.J. / Huang, S.C. / Puhalovich, T. / Du, Y. / Wittlin, S. / Nie, S. / Luth, M.R. / Ma, L. / Kim, M.S. / Pasaje, C.F.A. / Kumpornsin, K. / Giannangelo, C. / Houghton, F.J. / Churchyard, A. / Famodimu, M.T. / Barry, D.C. / Gillett, D.L. / Dey, S. / Kosasih, C.C. / Newman, W. / Niles, J.C. / Lee, M.C.S. / Baum, J. / Ottilie, S. / Winzeler, E.A. / Creek, D.J. / Williamson, N. / Parker, M.W. / Brand, S. / Langston, S.P. / Dick, L.R. / Griffin, M.D.W. / Gould, A.E. / Tilley, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188 KB | Display | ![]() |
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PDB format | ![]() | 123.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rorC ![]() 7rosC ![]() 7rotC ![]() 4qbtS 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: 41119.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-66I / {( | ||||
#3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.1-2.3 M ammonium sulfate, 2% acetone, 0.1 M NaH2PO4/K2HPO4, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→43.98 Å / Num. obs: 48890 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 33.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Rsym value: 0.081 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2547 / CC1/2: 0.467 / Rpim(I) all: 1.147 / Rrim(I) all: 3.024 / Rsym value: 2.795 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4QBT Resolution: 1.7→43.98 Å / SU ML: 0.2134 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 23.2572 Stereochemistry target values: GeoStd + Monomer Library + 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: 45.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.98 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 60.5914104558 Å / Origin y: 22.236189405 Å / Origin z: 42.3382386403 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 4 through 342) |