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- PDB-4qei: Two distinct conformational states of GlyRS captured in crystal l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qei | ||||||
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Title | Two distinct conformational states of GlyRS captured in crystal lattice | ||||||
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![]() | LIGASE/RNA / aminoacyl-tRNA synthetase / glycylation / glycyl-tRNA synthetase / tRNA ligase / LIGASE-RNA complex | ||||||
Function / homology | ![]() mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / protein dimerization activity / mitochondrial matrix / axon / mitochondrion / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, W. / Qin, X. / Deng, X. / Zhang, Q. / Li, Q. | ||||||
![]() | ![]() Title: Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis Authors: Deng, X. / Qin, X. / Chen, L. / Jia, Q. / Zhang, Y. / Zhang, Z. / Lei, D. / Ren, G. / Zhou, Z. / Wang, Z. / Li, Q. / Xie, W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.5 KB | Display | ![]() |
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PDB format | ![]() | 121.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 869.4 KB | Display | ![]() |
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Full document | ![]() | 882 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kqeC ![]() 4kr3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 71757.727 Da / Num. of mol.: 1 / Fragment: UNP residues 118-739 / Mutation: E71G, C157R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 22326.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the RNA is obtained from in vitro transcription / Source: (synth.) ![]() |
#3: Chemical | ChemComp-AMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 27% PEG600, 0.1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.875→50 Å / Num. all: 22411 / Num. obs: 22329 / % possible obs: 99.7 % / Observed criterion σ(I): 5.5 / Redundancy: 5.8 % / Biso Wilson estimate: 69.3 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.875→3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2205 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KR3 Resolution: 2.875→36.9 Å / FOM work R set: 0.7801 / SU ML: 0.33 / σ(F): 0 / Phase error: 27.56 / 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: 142.54 Å2 / Biso mean: 63.52 Å2 / Biso min: 25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.875→36.9 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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