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- PDB-6aa0: Crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (Tg... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aa0 | ||||||
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Title | Crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in Apo Form | ||||||
![]() | Prolyl-tRNA synthetase (ProRS) | ||||||
![]() | TRANSLATION / Toxoplasma gondii / Proly tRNA Synthetase / Apo-Form / Inhibitor-Bound Structural Comparison. | ||||||
Function / homology | ![]() proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mishra, S. / Kumari, S. / Sharma, A. / Yogavel, M. | ||||||
![]() | ![]() Title: Conformational heterogeneity in apo and drug-bound structures of Toxoplasma gondii prolyl-tRNA synthetase. Authors: Mishra, S. / Malhotra, N. / Kumari, S. / Sato, M. / Kikuchi, H. / 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 | ![]() | 377.1 KB | Display | ![]() |
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PDB format | ![]() | 309.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 62.8 KB | Display | |
Data in CIF | ![]() | 83.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a88C ![]() 5xifS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: Published |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980066 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→97.91 Å / Num. obs: 47193 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 74.67 Å2 / CC1/2: 0.996 / Χ2: 0.99 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3515 / CC1/2: 0.844 / Χ2: 1.02 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5xif Resolution: 3.2→69.932 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.11 Å2 / Biso mean: 76.9758 Å2 / Biso min: 29.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→69.932 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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