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Yorodumi- PDB-7fak: Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fak | ||||||
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Title | Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L96 and L-pro | ||||||
Components | Prolyl-tRNA synthetase (ProRS) | ||||||
Keywords | TRANSLATION/INHIBITOR / Inhibitor-Bound Structural Comparison / Multi-drug / TRANSLATION-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information 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 | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å | ||||||
Authors | Malhotra, N. / Mishra, S. / Yogavel, M. / Sharma, A. | ||||||
Funding support | India, 1items
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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 | 7fak.cif.gz | 220.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fak.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 7fak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/7fak ftp://data.pdbj.org/pub/pdb/validation_reports/fa/7fak | HTTPS FTP |
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-Related structure data
Related structure data | 7f98C 7f99C 7f9aC 7f9bC 7f9cC 7f9dC 7falC 7famC 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 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.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_057780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6JUK2 |
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-Non-polymers , 6 types, 302 molecules
#2: Chemical | ChemComp-1UI / | ||||
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#3: Chemical | ChemComp-PRO / | ||||
#4: Chemical | ChemComp-MES / | ||||
#5: Chemical | ChemComp-FMT / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus G2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→60.811 Å / Num. obs: 45141 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.125 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.89→1.94 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2157 / CC1/2: 0.5 / Rrim(I) all: 0.89 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6aa0 Resolution: 1.899→60.811 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 24.27 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.899→60.811 Å
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Refine LS restraints |
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LS refinement shell |
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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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