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Open data
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Basic information
Entry | Database: PDB / ID: 6oz5 | ||||||
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Title | Escherichia coli tRNA synthetase in complex with compound 3 | ||||||
![]() | (Phenylalanine--tRNA ligase ...) x 2 | ||||||
![]() | 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 / cytoplasm / cytosol 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 533.9 KB | Display | ![]() |
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PDB format | ![]() | 344.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p24C ![]() 6p26C ![]() 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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Unit cell |
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Components
-Phenylalanine--tRNA ligase ... , 2 types, 4 molecules ACBD
#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 |
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-Non-polymers , 6 types, 315 molecules ![](data/chem/img/VB3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% PEG 8,000, 200 mM MgCl2, 100 mM Tris-HCl pH 8.5, 2% 1,6-hexanediol, 3% 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: Oct 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→59.37 Å / Num. obs: 95661 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.997 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4659 / CC1/2: 0.516 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PCO Resolution: 2.5→58.23 Å / SU ML: 0.359 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9697 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: 59.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→58.23 Å
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Refine LS restraints |
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LS refinement shell |
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