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- PDB-8ke3: PylRS C-terminus domain mutant bound with D-3-trifluoromethylphen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ke3 | ||||||||||||
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Title | PylRS C-terminus domain mutant bound with D-3-trifluoromethylphenylalanine and AMPNP | ||||||||||||
![]() | Pyrrolysine--tRNA ligase | ||||||||||||
![]() | LIGASE / tRNA Synthetase | ||||||||||||
Function / homology | ![]() pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Weng, J.H. / Tsai, M.D. / Wang, Y.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Authors: Jiang, H.K. / Weng, J.H. / Wang, Y.H. / Tsou, J.C. / Chen, P.J. / Ko, A.A. / Soll, D. / Tsai, M.D. / Wang, Y.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 | ![]() | 81.5 KB | Display | ![]() |
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PDB format | ![]() | 51.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ke1C ![]() 8ke2C ![]() 8ke4C ![]() 8ke5C ![]() 8ke6C ![]() 2zceS 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: 31999.602 Da / Num. of mol.: 1 / Fragment: C-terminus domain / Mutation: N346G,C348Q,V401G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ANP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-FXC / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES buffer at pH 7.5, 10% PEG 8000, 10% Ethylene Glycerol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 27, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.899801→35 Å / Num. obs: 34993 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.8583536783 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Net I/σ(I): 21.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZCE Resolution: 1.89980982122→34.2612998565 Å / SU ML: 0.158762892065 / Cross valid method: FREE R-VALUE / σ(F): 1.36297285096 / Phase error: 19.969341506 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: 24.9292408815 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89980982122→34.2612998565 Å
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Refine LS restraints |
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LS refinement shell |
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