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- PDB-7ntz: Crystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ntz | ||||||||||||
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Title | Crystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant in Complex with the Reaction Intermediate Leu-AMP | ||||||||||||
![]() | Leucine--tRNA ligase | ||||||||||||
![]() | LIGASE / protein-ligand complex / Rossmann fold / tRNA synthetase | ||||||||||||
Function / homology | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Pang, L. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Authors: Pang, L. / Zanki, V. / Strelkov, S.V. / Van Aerschot, A. / Gruic-Sovulj, I. / Weeks, S.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 | ![]() | 323.7 KB | Display | ![]() |
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PDB format | ![]() | 258.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 821.4 KB | Display | ![]() |
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Full document | ![]() | 827.3 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ntyC ![]() 7nu0C ![]() 7nu1C ![]() 7nu2C ![]() 7nu3C ![]() 7nu4C ![]() 7nu5C ![]() 7nu6C ![]() 7nu7C ![]() 7nu8C ![]() 7nu9C ![]() 7nuaC ![]() 7nubC ![]() 7nucC ![]() 6q89S C: citing same article ( S: Starting model for refinement |
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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: 98143.266 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: L550A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-USB / [[( |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 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 8.0, 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 8.0, 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 5 mM ATP and 5 mM L-leucine 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: Jun 14, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.980118 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→108.71 Å / Num. obs: 55849 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Net I/σ(I): 14.1 / Num. measured all: 522825 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Q89 Resolution: 2.1→54.35 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.23 / Stereochemistry target values: ML
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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 max: 160.81 Å2 / Biso mean: 55.267 Å2 / Biso min: 26.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→54.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % 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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