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- PDB-7f9r: 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: 7f9r | ||||||
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Title | Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95, L-Proline and Febrifugine | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 224.5 KB | Display | ![]() |
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PDB format | ![]() | 174.3 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 ![]() 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 , 6 types, 178 molecules ![](data/chem/img/JE6.gif)
![](data/chem/img/9SF.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9SF.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JE6 / ~{ | ||||||
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#3: Chemical | ChemComp-9SF / | ||||||
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PRO / | #7: 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: 2.54 Å3/Da / Density % sol: 51.64 % |
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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 (midazole; 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 (midazole; 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 EIGER2 XE 16M / Detector: PIXEL / Date: Jul 8, 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: 1.83→51.34 Å / Num. obs: 51148 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2547 / CC1/2: 0.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XIQ Resolution: 1.83→35.721 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.25 / 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: 147.69 Å2 / Biso mean: 56.1521 Å2 / Biso min: 30.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→35.721 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: 15.1421 Å / Origin y: -0.1611 Å / Origin z: 8.1174 Å
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Refinement TLS group | Selection details: all |