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Yorodumi- PDB-2hrk: Structural basis of yeast aminoacyl-tRNA synthetase complex forma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hrk | ||||||
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Title | Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes | ||||||
Components |
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Keywords | ligase/RNA Binding Protein / protein complex protein interaction GST-fold / ligase-RNA Binding Protein COMPLEX | ||||||
Function / homology | Function and homology information methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule ...methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule / tRNA binding / mRNA binding / mitochondrion / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Simader, H. / Suck, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2006 Title: Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes. Authors: Simader, H. / Hothorn, M. / Kohler, C. / Basquin, J. / Simos, G. / Suck, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hrk.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hrk.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrk ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrk | HTTPS FTP |
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-Related structure data
Related structure data | 2hsmC 2hsnC 2hqtS 2hraS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is the binary complex. The asymmetric unit contains one biological unit. |
-Components
#1: Protein | Mass: 22765.432 Da / Num. of mol.: 1 / Fragment: Residues 1-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: GUS1 / Plasmid: pETm-derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46655, glutamate-tRNA ligase |
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#2: Protein | Mass: 14002.878 Da / Num. of mol.: 1 / Fragment: Residues 1-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ARC1 / Plasmid: pETm-derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46672 |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 30-35 % PEG 3350, 0.3-0.5 M NaSCN, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 29, 2006 / Details: Osmic VariMax Multilayer |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→45 Å / Num. obs: 20000 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.038 / Net I/σ(I): 27.45 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.75 / Num. unique all: 1396 / Rsym value: 0.28 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HRA PDB entry 2HQT Resolution: 2.05→45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.252 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.221 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.461 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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