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Yorodumi- PDB-4q2t: Crystal structure of Arginyl-tRNA synthetase complexed with L-arginine -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q2t | ||||||
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Title | Crystal structure of Arginyl-tRNA synthetase complexed with L-arginine | ||||||
Components | Arginine--tRNA ligase, cytoplasmic | ||||||
Keywords | LIGASE / HIGH region / arginine-tRNA ligase activity / arginine binding / tRNA binding | ||||||
Function / homology | Function and homology information arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / arginine binding / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA binding ...arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / arginine binding / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA binding / cadherin binding / nucleolus / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kim, H.S. / Jo, C.H. / Cha, S.Y. / Han, A.R. / Hwang, K.Y. | ||||||
Citation | Journal: Febs Lett. / Year: 2014 Title: The crystal structure of arginyl-tRNA synthetase from Homo sapiens Authors: Kim, H.S. / Cha, S.Y. / Jo, C.H. / Han, A.R. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q2t.cif.gz | 249.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2t.ent.gz | 200.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2t ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2t | HTTPS FTP |
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-Related structure data
Related structure data | 4q2xC 4q2yC 1bs2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: -1 - 588 / Label seq-ID: 18 - 607
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-Components
#1: Protein | Mass: 69347.727 Da / Num. of mol.: 2 / Mutation: H438R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RARS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P54136, arginine-tRNA ligase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS ISOFORM MONOMERIC, P54136-2. | |
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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: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.085mM Sodium citrate tribasic dehydrate, 24% PEG4000, 0.17M Ammonium acetate, 15% Glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 55170 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 44.33 Å2 / Rmerge(I) obs: 0.075 / Χ2: 2.228 / Net I/σ(I): 13.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BS2 Resolution: 2.4→38.91 Å / FOM work R set: 0.7766 / SU ML: 0.36 / σ(F): 1.5 / Phase error: 28.76 / 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: 114.63 Å2 / Biso mean: 47.37 Å2 / Biso min: 21.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→38.91 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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