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Yorodumi- PDB-5fog: Crystal structure of hte Cryptosporidium muris cytosolic leucyl-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fog | ||||||
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Title | Crystal structure of hte Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of norvaline (Nv2AA) | ||||||
Components | LEUCYL-TRNA SYNTHETASE | ||||||
Keywords | LYASE / CRYPTOSPORIDIUM / LEUCINE-TRNA LIGASE (LEURS) ACTIVITY / ATP + L-LEUCINE + TRNA(LEUCINE) GIVE AMP + DIPHOSPHATE + L-LEUCYL-TRNA(LEUCINE) / POST-TRANSFER EDITING ACTIVITY OF LEURS / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / NOVEL BORON INHIBITORS OF THE EDITING SITE OF LEURS | ||||||
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 | CRYPTOSPORIDIUM MURIS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Palencia, A. / Liu, R.J. / Lukarska, M. / Gut, J. / Bougdour, A. / Touquet, B. / Wang, E.D. / Alley, M.R.K. / Rosenthal, P.J. / Hakimi, M.A. / Cusack, S. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2016 Title: Cryptosporidium and Toxoplasma Parasites are Inhibited by a Benzoxaborole Targeting Leucyl-tRNA Synthetase. Authors: Palencia, A. / Liu, R. / Lukarska, M. / Gut, J. / Bougdour, A. / Touquet, B. / Wang, E. / Li, X. / Alley, M.R.K. / Freund, Y.R. / Rosenthal, P.J. / Hakimi, M. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fog.cif.gz | 240.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fog.ent.gz | 193.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5fog ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5fog | HTTPS FTP |
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-Related structure data
Related structure data | 5folC 5fomC 5fonC 2wfgS 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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Unit cell |
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-Components
#1: Protein | Mass: 32973.277 Da / Num. of mol.: 4 / Fragment: EDITING DOMAIN, UNP RESIDUES 254-541 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRYPTOSPORIDIUM MURIS (eukaryote) / Strain: RN66 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): DE3 BL21 RIL / References: UniProt: B6AA20, leucine-tRNA ligase #2: Chemical | ChemComp-VRT / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 3.4 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | pH: 6.9 Details: 0.1 M KNO3 PH 6.9, 22% (W/V) PEG 3350. 20 % ETHYLENE GLYCOL AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 81817 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.9 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WFG Resolution: 2.3→101.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.895 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 46.977 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→101.76 Å
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Refine LS restraints |
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