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Yorodumi- PDB-7fam: Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fam | ||||||
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Title | Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L97 and L-pro | ||||||
Components | Prolyl-tRNA synthetase (ProRS) | ||||||
Keywords | TRANSLATION / Inhibitor-Bound Structural Comparison / Multi-drug | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Mishra, S. / Malhotra, N. / Yogavel, M. / Sharma, A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2023 Title: Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. Authors: Yogavel, M. / Bougdour, A. / Mishra, S. / Malhotra, N. / Chhibber-Goel, J. / Bellini, V. / Harlos, K. / Laleu, B. / Hakimi, M.A. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fam.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fam.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 7fam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/7fam ftp://data.pdbj.org/pub/pdb/validation_reports/fa/7fam | HTTPS FTP |
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-Related structure data
Related structure data | 7f98C 7f99C 7f9aC 7f9bC 7f9cC 7f9dC 7fakC 7falC 7fanC 7vc1C 7vc2C 7vc3C 6aa0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_057780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6JUK2 |
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#2: Chemical | ChemComp-1XK / |
#3: Chemical | ChemComp-PRO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus H3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9804 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9804 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→52.874 Å / Num. obs: 22556 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.985 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.42→2.48 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1640 / CC1/2: 0.898 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6aa0 Resolution: 2.42→52.874 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 25.58 / 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: 116.52 Å2 / Biso mean: 57.7333 Å2 / Biso min: 28.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.42→52.874 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 / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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