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Yorodumi- PDB-7f9u: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f9u | ||||||
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Title | Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Halofuginone | ||||||
Components | Prolyl-tRNA synthetase (ProRS) | ||||||
Keywords | LIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / DOUBLE DRUG / LIGASE / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Manickam, Y. / Malhotra, N. / Sharma, A. | ||||||
Citation | Journal: To Be Published Title: TgPRS with double inhibitors Authors: Malhotra, N. / Manickam, Y. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f9u.cif.gz | 788 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f9u.ent.gz | 648.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f9u_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7f9u_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7f9u_validation.xml.gz | 65.7 KB | Display | |
Data in CIF | 7f9u_validation.cif.gz | 90.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/7f9u ftp://data.pdbj.org/pub/pdb/validation_reports/f9/7f9u | HTTPS FTP |
-Related structure data
Related structure data | 7f9pC 7f9qC 7f9rC 7f9sC 7f9tC 7f9vC 7vc5C 5xiqS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 57937.258 Da / Num. of mol.: 4 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, 72 molecules
#2: Chemical | ChemComp-HFG / #3: Chemical | ChemComp-1TI / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate ), 0.1 M Buffer (Sodium HEPES, MOPS), 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.15 |
Reflection | Resolution: 2.8→100.93 Å / Num. obs: 56889 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2092 / CC1/2: 0.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XIQ Resolution: 2.8→76.573 Å / Cross valid method: THROUGHOUT / σ(F): 3.47 / Phase error: 26.32 / Stereochemistry target values: TWIN_LSQ_F
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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: 215.66 Å2 / Biso mean: 33.3552 Å2 / Biso min: 13.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→76.573 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 38.9614 Å / Origin y: -1.0273 Å / Origin z: 15.9088 Å
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Refinement TLS group | Selection details: all |