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- PDB-5xil: Crystal Structure of Leishmania major Prolyl-tRNA Synthetase (LmPRS) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xil | ||||||
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Title | Crystal Structure of Leishmania major Prolyl-tRNA Synthetase (LmPRS) | ||||||
![]() | Putative prolyl-tRNA synthetase | ||||||
![]() | 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 | ![]() | 118.3 KB | Display | ![]() |
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PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444 KB | Display | ![]() |
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Full document | ![]() | 445.8 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xifC ![]() 5xigC ![]() 5xihC ![]() 5xiiC ![]() 5xijC ![]() 5xikC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 58453.508 Da / Num. of mol.: 1 / Fragment: UNP residues 223-731 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4QDS0, isoleucine-tRNA ligase, alanine-tRNA ligase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium acetate and 20%(w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.289 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 43411 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Χ2: 0.9 / Net I/σ(I): 13.9 / Num. measured all: 270270 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TWA Resolution: 1.9→40.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.784 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.123 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.13 Å2 / Biso mean: 23.183 Å2 / Biso min: 8.29 Å2
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Refinement step | Cycle: final / Resolution: 1.9→40.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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