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Yorodumi- PDB-6q89: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q89 | ||||||||||||
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Title | Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Leucyl)-Sulfamoyl)Adenosine | ||||||||||||
Components | Leucine--tRNA ligase | ||||||||||||
Keywords | LIGASE / protein-inhibitor complex / Rossmann fold / tRNA synthetase | ||||||||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||||||||
Authors | Pang, L. / De Graef, S. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases. Authors: Nautiyal, M. / De Graef, S. / Pang, L. / Gadakh, B. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q89.cif.gz | 347.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q89.ent.gz | 279.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q89_validation.pdf.gz | 745.8 KB | Display | wwPDB validaton report |
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Full document | 6q89_full_validation.pdf.gz | 749.5 KB | Display | |
Data in XML | 6q89_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 6q89_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q89 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q89 | HTTPS FTP |
-Related structure data
Related structure data | 6hb5C 6hb6C 6hb7C 6i5yC 6q8aC 6q8bC 6q8cC 3zjuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Neisseria gonorrhoeae (bacteria) Gene: leuS, WHOK_00006, WHOM_00006, WHOO_00006, WHOP_00006, WHOU_00006, WHOW_00006, WHOX_00006, WHOY_00006, WHOZ_00006 Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: A0A1D3HNX6, leucine-tRNA ligase |
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-Non-polymers , 5 types, 212 molecules
#2: Chemical | ChemComp-LSS / |
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#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.92 % |
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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 1 mM 5'-O-(N-(L-Leucyl)-Sulfamoyl)Adenosine 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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 15, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.09→82.93 Å / Num. obs: 56400 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 43.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Net I/σ(I): 13.8 / Num. measured all: 419417 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A model generated from 3ZJU Resolution: 2.21→77.96 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.46 Å2 / Biso mean: 55.2037 Å2 / Biso min: 23.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.21→77.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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