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- PDB-5fon: Crystal structure of the Cryptosporidium muris cytosolic leucyl-t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fon | ||||||
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Title | Crystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain (apo structure) | ||||||
![]() | (LEUCYL-TRNA SYNTHETASE) x 2 | ||||||
![]() | 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 | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 441.8 KB | Display | ![]() |
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PDB format | ![]() | 372 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 460.4 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fogC ![]() 5folC ![]() 5fomC ![]() 2wfgS C: citing same article ( S: Starting model for refinement |
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Similar 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32916.227 Da / Num. of mol.: 3 / Fragment: EDITING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 32930.254 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 0.1 M MES (PH 6.8), 2% ETHANOL AND 10% (W/V) PEG 20000. 20% (V/V) ETHYLENE GLYCOL WAS USED AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.7→48 Å / Num. obs: 51501 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.7→2.84 Å / Redundancy: 9 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.7 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WFG Resolution: 2.7→48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 26.826 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 90.569 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→48 Å
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Refine LS restraints |
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