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- PDB-6yks: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yks | ||||||||||||
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Title | Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11d | ||||||||||||
![]() | Leucine--tRNA ligase | ||||||||||||
![]() | LIGASE / protein-inhibitor complex / Rossmann fold / tRNA synthetase | ||||||||||||
Function / homology | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Pang, L. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors. Authors: De Ruysscher, D. / Pang, L. / Lenders, S.M.G. / Cappoen, D. / Cos, P. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344 KB | Display | ![]() |
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PDB format | ![]() | 275.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 711.9 KB | Display | ![]() |
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Full document | ![]() | 714.3 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ykkC ![]() 6yklC ![]() 6yknC ![]() 6ykoC ![]() 6ykqC ![]() 6yktC ![]() 6ykuC ![]() 6ykvC ![]() 6ykwC ![]() 6ykxC ![]() 7a0pC ![]() 6q89S C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 98185.344 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: D454N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A5K1KQ39, UniProt: Q5FAJ3*PLUS, leucine-tRNA ligase |
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-Non-polymers , 5 types, 406 molecules ![](data/chem/img/OVT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OVT / [( | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % / Mosaicity: 0.17 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0. ...Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0.75:1.0:0.25 (v/v) ratio. The seed stock was prepared in the same crystallization buffer. Suitable crystals were soaked with 2 mM synthesized compound 11d in an equilvalent precipitant solution supplemented with 22% v/v ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.980112 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→112.09 Å / Num. obs: 66445 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.028 / Rrim(I) all: 0.079 / Net I/σ(I): 14.6 / Num. measured all: 533986 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Q89 Resolution: 1.97→65.603 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.4 Å2 / Biso mean: 42.8199 Å2 / Biso min: 19.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→65.603 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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