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Yorodumi- PDB-6l3y: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falcip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l3y | ||||||
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Title | Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-C | ||||||
Components | Lysine--tRNA ligase | ||||||
Keywords | PROTEIN BINDING/INHIBITOR / Inhibitor / Cladosporin analog / Stereochemistry / PROTEIN BINDING / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | Function and homology information lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Babbar, P. / Sharma, A. / Mishra, S. / Manickam, Y. / Harlos, K. | ||||||
Funding support | India, 1items
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Citation | Journal: Chembiochem / Year: 2021 Title: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B Authors: Babbar, P. / Sato, M. / Manickam, Y. / Mishra, S. / Harlos, K. / Gupta, S. / Parvez, S. / Kikuchi, H. / Sharma, A. #1: Journal: J. Struct. Funct. Genomics / Year: 2014 Title: Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin. Authors: Khan, S. / Sharma, A. / Belrhali, H. / Yogavel, M. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l3y.cif.gz | 208.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l3y.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/6l3y ftp://data.pdbj.org/pub/pdb/validation_reports/l3/6l3y | HTTPS FTP |
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-Related structure data
Related structure data | 6l4qC 4pg3S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 58706.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1350100 / Plasmid: petm41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IDJ8, lysine-tRNA ligase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.13 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.09M NPS-0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic,0.3M Ammonium sulfate. 1.0M Buffer-pH6.5- Imidazole; MES monohydrate (acid) Precipitant Mix-25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→149.921 Å / Num. obs: 25891 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.989 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.898→2.948 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1293 / CC1/2: 0.446 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PG3 Resolution: 3.1→74.96 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.32 / 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: 117.58 Å2 / Biso mean: 57.6733 Å2 / Biso min: 26.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→74.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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