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Yorodumi- PDB-5fod: Crystal structure of the P.falciparum cytosolic leucyl-tRNA synth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fod | ||||||
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Title | Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P1) containing deletions of insertions 1 and 3 | ||||||
Components | LEUCYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / P.FALCIPARUM / LEUCINE-TRNA LIGASE (LEURS) ACTIVITY / ATP + L-LEUCINE + TRNA(LEUCINE) GIVES AMP + DIPHOSPHATE + L-LEUCYL-TRNA(LEUCINE) / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / NOVEL BORON INHIBITORS OF LEURS | ||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Palencia, A. / Sonoiki, E. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Gut, J. / Legac, J. / Cooper, R. ...Palencia, A. / Sonoiki, E. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Gut, J. / Legac, J. / Cooper, R. / Alley, M.R.K. / Freund, Y.R. / DeRisi, J. / Cusack, S. / Rosenthal, P.J. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2016 Title: Anti-Malarial Benzoxaboroles Target P. Falciparum Leucyl-tRNA Synthetase. Authors: Sonoiki, E. / Palencia, A. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Zhang, Y.K. / Choi, W. / Gut, J. / Legac, J. / Cooper, R. / Alley, M.R. / Freund, Y.R. / Derisi, J. ...Authors: Sonoiki, E. / Palencia, A. / Guo, D. / Ahyong, V. / Dong, C. / Li, X. / Hernandez, V.S. / Zhang, Y.K. / Choi, W. / Gut, J. / Legac, J. / Cooper, R. / Alley, M.R. / Freund, Y.R. / Derisi, J. / Cusack, S. / Rosenthal, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fod.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fod.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5fod ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5fod | HTTPS FTP |
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-Related structure data
-Links
-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: 39833.352 Da / Num. of mol.: 2 Fragment: EDITING DOMAIN, UNP RESIDUES 274-329,361-474,521-687 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: C6KT64, leucine-tRNA ligase #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES (PH 7.5), 20% (W/V) PEG 10000, AND 8% ETHYLENEGLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. obs: 62051 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.8 / % possible all: 88 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PLASMODIUM KNOWLESI LEURS EDITING DOMAIN Resolution: 1.7→60.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.95 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PRESENCE OF NCS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→60.16 Å
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Refine LS restraints |
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