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Yorodumi- PDB-7v8j: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v8j | ||||||
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Title | Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with the reaction intermediates proline-adenylate (Pro-AMP) and pyrophosphate | ||||||
Components | Prolyl-tRNA synthetase | ||||||
Keywords | LIGASE / PROTEIN TRANSLATION / L-Proline / PRS / Toxoplasmosis | ||||||
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: 2.519 Å | ||||||
Authors | Manickam, Y. / Malhotra, N. / Sharma, A. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with the reaction intermediates proline-adenylate (Pro-AMP) and pyrophosphate Authors: Manickam, Y. / Malhotra, N. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v8j.cif.gz | 403.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v8j.ent.gz | 324.2 KB | Display | PDB format |
PDBx/mmJSON format | 7v8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/7v8j ftp://data.pdbj.org/pub/pdb/validation_reports/v8/7v8j | HTTPS FTP |
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-Related structure data
Related structure data | 5xifS S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 2 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, proline-tRNA ligase |
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-Non-polymers , 5 types, 174 molecules
#2: Chemical | ChemComp-PR8 / | ||||
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#3: Chemical | ChemComp-PPV / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PRO / | #6: 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: 2.79 Å3/Da / Density % sol: 55.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.12 M Ethylene glycols (0.3M Diethylene glycol, 0.3M Triethylene glycol, 0.3M Tetraethylene glycol, 0.3M Pentaethylene glycol), 0.1 M Buffer (Imidazole, MES monohydrate), 30% v/v ...Details: 0.12 M Ethylene glycols (0.3M Diethylene glycol, 0.3M Triethylene glycol, 0.3M Tetraethylene glycol, 0.3M Pentaethylene glycol), 0.1 M Buffer (Imidazole, MES monohydrate), 30% v/v Precipitant mix (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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.519→47.51 Å / Num. obs: 43233 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.992 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.519→2.58 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3038 / CC1/2: 0.606 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XIF Resolution: 2.519→47.504 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.06 / 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: 123.36 Å2 / Biso mean: 53.2808 Å2 / Biso min: 32.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.519→47.504 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: -14.8721 Å / Origin y: -16.2053 Å / Origin z: -34.1176 Å
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Refinement TLS group | Selection details: all |