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- PDB-7f96: Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f96 | ||||||
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Title | Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95 | ||||||
![]() | Proline--tRNA ligase | ||||||
![]() | LIGASE / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS | ||||||
Function / homology | ![]() Ala-tRNA(Pro) hydrolase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mishra, S. / Malhotra, N. / Yogavel, M. / Sharma, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development Authors: Mishra, S. / Malhotra, N. / Laleu, B. / Chakraborti, S. / Yogavel, M. / 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 | ![]() | 216.6 KB | Display | ![]() |
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PDB format | ![]() | 171.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7f97C ![]() 4ydqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 57801.188 Da / Num. of mol.: 1 / Fragment: UNP residues 254-746 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-JE6 / ~{ |
#3: Chemical | ChemComp-PRO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v ...Details: 0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v Precipitant Mix (40% v/v Ethylene glycol; 20% w/v PEG 8000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.577→48.542 Å / Num. obs: 25534 / % possible obs: 99.4 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.084 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.58→2.64 Å / Redundancy: 17.1 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1720 / CC1/2: 0.93 / Rrim(I) all: 0.844 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YDQ Resolution: 2.577→38.542 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.82 Å2 / Biso mean: 62.1279 Å2 / Biso min: 29.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.577→38.542 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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