+Open data
-Basic information
Entry | Database: PDB / ID: 4kqe | ||||||
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Title | The mutant structure of the human glycyl-tRNA synthetase E71G | ||||||
Components | Glycine--tRNA ligase | ||||||
Keywords | LIGASE / Rossmann fold / aminoacylation / tRNA-Gly | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.739 Å | ||||||
Authors | Qin, X. / Hao, Z. / Tian, Q. / Zhang, Z. / Zhou, C. / Xie, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kqe.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kqe.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 4kqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kqe_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 4kqe_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 4kqe_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4kqe_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/4kqe ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kqe | HTTPS FTP |
-Related structure data
Related structure data | 4qeiC 2pmeS 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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-Components
#1: Protein | Mass: 78632.766 Da / Num. of mol.: 1 / Fragment: UNP residues 55-739 / Mutation: E71G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GARS / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41250, glycine-tRNA ligase |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 3.27 Å3/Da / Density % sol: 62.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M ammonium citrate, 17% PEG3350, 0.1M Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.739→50 Å / Num. all: 28342 / Num. obs: 28122 / % possible obs: 99.3 % / Observed criterion σ(I): 2.5 / Redundancy: 7.1 % / Biso Wilson estimate: 49.81 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 7 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.5 / Num. unique all: 28038 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PME Resolution: 2.739→34.665 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8101 / SU ML: 0.28 / σ(F): 1.35 / Phase error: 25.15 / 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: 163.61 Å2 / Biso mean: 56.6126 Å2 / Biso min: 13.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.739→34.665 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: 10
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