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- PDB-5xii: Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (Tg... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xii | ||||||
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Title | Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 6 | ||||||
![]() | Prolyl-tRNA synthetase (ProRS) | ||||||
![]() | LIGASE / Protein Translation / PRS / Synthetase / Inhibitor / Infectious Disease | ||||||
Function / homology | ![]() proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jain, V. / Manickam, Y. / Sharma, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 419 KB | Display | ![]() |
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PDB format | ![]() | 336.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 75.3 KB | Display | |
Data in CIF | ![]() | 105.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xifC ![]() 5xigC ![]() 5xihC ![]() 5xijC ![]() 5xikC ![]() 5xilC ![]() 5xioC ![]() 5xipC ![]() 5xiqC ![]() 4twaS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 4 / Mutation: UNP residues 334-830 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 50611 / Me49 / Gene: TGME49_219850 / Plasmid: PETM41 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 750 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/86X.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/86X.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-86X / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.83 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.17→50 Å / Num. obs: 123090 / % possible obs: 98.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.031 / Rrim(I) all: 0.052 / Χ2: 0.82 / Net I/σ(I): 11 / Num. measured all: 337845 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TWA Resolution: 2.17→40.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2121 / WRfactor Rwork: 0.1636 / FOM work R set: 0.8479 / SU B: 5.184 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2272 / SU Rfree: 0.1899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 105.82 Å2 / Biso mean: 33.867 Å2 / Biso min: 7.66 Å2
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Refinement step | Cycle: final / Resolution: 2.17→40.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.175→2.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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