[English] 日本語
Yorodumi- PDB-5v58: Crystal structure of human prolyl-tRNA synthetase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v58 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human prolyl-tRNA synthetase in complex with Aze-SA | ||||||
Components | Bifunctional glutamate/proline--tRNA ligase | ||||||
Keywords | LIGASE / aminoacyl-tRNA synthetase / non-proteinogenic amino acids | ||||||
Function / homology | Function and homology information regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / RNA stem-loop binding / GAIT complex / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / protein-containing complex assembly / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Zhou, H. / Song, Y. / Schimmel, P. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid. Authors: Song, Y. / Zhou, H. / Vo, M.N. / Shi, Y. / Nawaz, M.H. / Vargas-Rodriguez, O. / Diedrich, J.K. / Yates, J.R. / Kishi, S. / Musier-Forsyth, K. / Schimmel, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5v58.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5v58.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 5v58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/5v58 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/5v58 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5v59C 4hvcS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59063.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli) References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase |
---|---|
#2: Chemical | ChemComp-8X1 / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation Details: 9% PEG3350, 250 mM sodium nitrate, 100 mM 3-(1-pyridino)-1-propane sulfonate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.59→50 Å / Num. obs: 14793 / % possible obs: 96.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.057 / Χ2: 0.963 / Net I/σ(I): 19 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4HVC Resolution: 2.59→35.54 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.639 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.378 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.51 Å2 / Biso mean: 59.398 Å2 / Biso min: 20 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.59→35.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.588→2.655 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|