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Open data
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Basic information
Entry | Database: PDB / ID: 6p26 | ||||||
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Title | Escherichia coli tRNA synthetase in complex with compound 1 | ||||||
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![]() | LIGASE / Inhibitor / Aminoacyl-tRNA synthetase / PheRS / Antibacterial | ||||||
Function / homology | ![]() phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kahne, D. / Baidin, V. / Owens, T.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Simple Secondary Amines Inhibit Growth of Gram-Negative Bacteria through Highly Selective Binding to Phenylalanyl-tRNA Synthetase. Authors: Baidin, V. / Owens, T.W. / Lazarus, M.B. / Kahne, D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 520.9 KB | Display | ![]() |
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PDB format | ![]() | 339.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6oz5C ![]() 6p24C ![]() 6p8tC ![]() 3pcoS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 37318.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pheS, D8B36_10295 / Production host: ![]() ![]() References: UniProt: A0A387D3L6, UniProt: P08312*PLUS, phenylalanine-tRNA ligase #2: Protein | Mass: 87483.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pheT, D8B36_10300 / Production host: ![]() ![]() References: UniProt: A0A387D0Y5, UniProt: P07395*PLUS, phenylalanine-tRNA ligase #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16% PEG 8,000, 200 mM MgCl2, 100 mM Tris-HCl pH8.5, 3% 1,6-hexanediol, 2% D-Galactose |
-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: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.16→82.27 Å / Num. obs: 47360 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 68.61 Å2 / CC1/2: 0.979 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.16→3.27 Å / Num. unique obs: 4527 / CC1/2: 0.366 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PCO Resolution: 3.16→82.27 Å / SU ML: 0.4406 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9338 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: 61.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.16→82.27 Å
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Refine LS restraints |
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LS refinement shell |
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