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- PDB-6p8t: Acinetobacter baumannii tRNA synthetase in complex with compound 1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p8t | ||||||
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Title | Acinetobacter baumannii tRNA synthetase in complex with compound 1 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 935.4 KB | Display | ![]() |
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PDB format | ![]() | 613.8 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 ![]() 6p26C ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 87791.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: pheT, HMPREF0010_01651 / Production host: ![]() ![]() ![]() ![]() #2: Protein | Mass: 37219.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: pheS, HMPREF0010_01652 / Production host: ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-NO4 / #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 17% PEG 8,000; 200 mM Mg(OAc)2; 100 mM NaCacodylate pH 6.2; 8 mM MgCl2; 8% 1,2,4-Butanetriol |
-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: Jul 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.15→19.923 Å / Num. obs: 99384 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 95.74 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.15→3.2 Å / Num. unique obs: 4674 / CC1/2: 0.266 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3PCO Resolution: 3.15→19.92 Å / SU ML: 0.4755 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.6324 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: 100.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→19.92 Å
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Refine LS restraints |
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LS refinement shell |
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