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Yorodumi- PDB-5fom: Crystal structure of the Cryptosporidium muris cytosolic leucyl-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fom | ||||||
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Title | Crystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with the adduct AMP-AN6426 | ||||||
Components | LEUCYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / 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: 2.1 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 | 5fom.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fom.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5fom ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5fom | HTTPS FTP |
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-Related structure data
Related structure data | 5fogC 5folC 5fonC 2wfgS 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
#1: Protein | Mass: 32916.227 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN 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): BL21(DE3) / Variant (production host): RIL / References: UniProt: B6AA20, leucine-tRNA ligase |
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#2: Chemical | ChemComp-A2H / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 1.4 M SODIUM/POTASSIUM PHOSPHATE PH 5.5. 20% GLYCEROL WAS USED AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→60.64 Å / Num. obs: 21974 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.6 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WFG Resolution: 2.1→60.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.146 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.169 / 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: 55.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→60.64 Å
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Refine LS restraints |
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