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- PDB-7f9t: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f9t | ||||||
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Title | Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 and Halofuginone | ||||||
![]() | Prolyl-tRNA synthetase (ProRS) | ||||||
![]() | LIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / DOUBLE DRUG / LIGASE / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | ![]() proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malhotra, N. / Manickam, Y. / Sharma, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: TgPRS with double inhibitors Authors: Malhotra, N. / Manickam, Y. / 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 | ![]() | 446.5 KB | Display | ![]() |
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PDB format | ![]() | 359.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7f9pC ![]() 7f9qC ![]() 7f9rC ![]() 7f9sC ![]() 7f9uC ![]() 7f9vC ![]() 7vc5C ![]() 5xiqS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 800 molecules ![](data/chem/img/1XK.gif)
![](data/chem/img/HFG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HFG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MES / | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-FMT / #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Carboxylic acids (0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate), 0.1 M Buffer ...Details: 0.1 M Carboxylic acids (0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate), 0.1 M Buffer (Imidazole; MES monohydrate), 30 % v/v Precipitant (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 XE 16M / Detector: PIXEL / Date: Jul 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.489→62.92 Å / Num. obs: 203943 / % possible obs: 96.4 % / Redundancy: 3.6 % / CC1/2: 1 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.49→1.51 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9732 / CC1/2: 0.6 / % possible all: 91.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XIQ Resolution: 1.489→45.067 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.13 / 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: 210.93 Å2 / Biso mean: 33.2848 Å2 / Biso min: 16.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.489→45.067 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 / Origin x: -7.6945 Å / Origin y: -26.2804 Å / Origin z: 7.5355 Å
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Refinement TLS group |
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