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- PDB-7f9p: 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: 7f9p | |||||||||
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Title | Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95 and azetidine | |||||||||
![]() | Prolyl-tRNA synthetase (ProRS) | |||||||||
![]() | LIGASE / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / DOUBLE DRUG | |||||||||
Function / homology | ![]() proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Manickam, Y. / Malhotra, N. / Sharma, A. | |||||||||
![]() | ![]() 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 | ![]() | 233.5 KB | Display | ![]() |
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PDB format | ![]() | 183.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.9 KB | Display | ![]() |
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Full document | ![]() | 757.9 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f9qC ![]() 7f9rC ![]() 7f9sC ![]() 7f9tC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 420 molecules ![](data/chem/img/JE6.gif)
![](data/chem/img/02A.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/02A.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JE6 / ~{ | ||
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#3: Chemical | ChemComp-02A / ( | ||
#4: Chemical | ChemComp-MES / | ||
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine), 0.1 M Buffer (Imidazole; MES monohydrate) and 30 % v/v ...Details: 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine), 0.1 M Buffer (Imidazole; MES monohydrate) and 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 PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→69.49 Å / Num. obs: 79294 / % possible obs: 98.5 % / Redundancy: 6.2 % / CC1/2: 1 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.57→1.6 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3363 / CC1/2: 0.7 / % possible all: 83.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XIQ Resolution: 1.57→51.32 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.15 / 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: 85.32 Å2 / Biso mean: 31.2558 Å2 / Biso min: 14.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→51.32 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: 40.2255 Å / Origin y: 1.024 Å / Origin z: 14.9309 Å
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Refinement TLS group | Selection details: all |