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- PDB-7vc5: 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: 7vc5 | ||||||
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Title | Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Febrifugine (FF) at 1.61 A resolution | ||||||
![]() | 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. | ||||||
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 | ![]() | 232.1 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7f9pC ![]() 7f9qC ![]() 7f9rC ![]() 7f9sSC ![]() 7f9tC ![]() 7f9uC ![]() 7f9vC 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
-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, 318 molecules ![](data/chem/img/1TI.gif)
![](data/chem/img/9SF.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9SF.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-1TI / | ||||
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#3: Chemical | ChemComp-9SF / | ||||
#4: Chemical | ChemComp-MES / | ||||
#5: Chemical | ChemComp-EDO / #6: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.42 % |
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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 and 0.2M DL-Serine), 0.1 M Buffer (Imidazole; MES monohydrate), 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 and 0.2M DL-Serine), 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 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: 1.61→60.38 Å / Num. obs: 74455 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 6.6 % / Num. unique obs: 3674 / CC1/2: 0.3 / Rrim(I) all: 2.511 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7F9S Resolution: 1.612→53.562 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.24 / 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: 96.66 Å2 / Biso mean: 43.699 Å2 / Biso min: 22.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.612→53.562 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: 15.1759 Å / Origin y: -0.1602 Å / Origin z: 8.2585 Å
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Refinement TLS group | Selection details: all |