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Yorodumi- PDB-5xik: Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (Tg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xik | ||||||
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Title | Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with tetrahydro quinazolinone febrifugine | ||||||
Components | Prolyl-tRNA synthetase (ProRS) | ||||||
Keywords | LIGASE / Protein Translation / PRS / Synthetase / Inhibitor / Infectious Disease | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Jain, V. / Manickam, Y. / Sharma, A. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis Authors: Jain, V. / Yogavel, M. / Kikuchi, H. / Oshima, Y. / Hariguchi, N. / Matsumoto, M. / Goel, P. / Touquet, B. / Jumani, R.S. / Tacchini-Cottier, F. / Harlos, K. / Huston, C.D. / Hakimi, M.A. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xik.cif.gz | 399.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xik.ent.gz | 320.1 KB | Display | PDB format |
PDBx/mmJSON format | 5xik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xik_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 5xik_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 5xik_validation.xml.gz | 67.7 KB | Display | |
Data in CIF | 5xik_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/5xik ftp://data.pdbj.org/pub/pdb/validation_reports/xi/5xik | HTTPS FTP |
-Related structure data
Related structure data | 5xifC 5xigC 5xihC 5xiiC 5xijC 5xilC 5xioC 5xipC 5xiqC 4twaS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 4 / Fragment: UNP residues 334-830 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote) Strain: ATCC 50611 / Me49 / Gene: TGME49_219850 / Plasmid: PETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: S8G8I1, proline-tRNA ligase |
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-Non-polymers , 5 types, 226 molecules
#2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-87C / #5: Chemical | ChemComp-CL / #6: 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: 2.66 Å3/Da / Density % sol: 53.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each divalent cation and 0.1M MOPS/HEPES-Na |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96725 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 2, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96725 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 80691 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Χ2: 0.837 / Net I/σ(I): 7.6 / Num. measured all: 266115 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TWA Resolution: 2.5→43.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.1741 / FOM work R set: 0.8383 / SU B: 8.678 / SU ML: 0.195 / SU R Cruickshank DPI: 0.5546 / SU Rfree: 0.2889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.289 / 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 max: 109.46 Å2 / Biso mean: 37.618 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.5→43.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.504→2.569 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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