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- PDB-5fod: Crystal structure of the P.falciparum cytosolic leucyl-tRNA synth... -
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Open data
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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 | ||||||
![]() | LEUCYL-TRNA SYNTHETASE | ||||||
![]() | 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 | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141 KB | Display | ![]() |
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PDB format | ![]() | 110.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
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Full document | ![]() | 443.7 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() Strain: 3D7 / Plasmid: PETM-11 / Production host: ![]() ![]() #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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