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Yorodumi- PDB-2zxf: Crystal structure of human glycyl-trna synthetase (GLYRS) in comp... -
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-Basic information
Entry | Database: PDB / ID: 2zxf | ||||||
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Title | Crystal structure of human glycyl-trna synthetase (GLYRS) in complex with AP4A (cocrystallized with AP4A) | ||||||
Components | Glycyl-tRNA synthetaseGlycine—tRNA ligase | ||||||
Keywords | LIGASE / AP4A / glycine / ATP / GLY-AMP / tRNA / aminoacyl-tRNA synthetase / ATP-binding / charcot-marie-tooth disease / disease mutation / nucleotide-binding / phosphoprotein / protein biosynthesis | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Guo, R.T. / Yang, X.L. / Schimmel, P. | ||||||
Citation | Journal: To be Published Title: Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis Authors: Guo, R.T. / Chong, Y.E. / Guo, M. / Yang, X.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxf.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxf.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 2zxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxf ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxf | HTTPS FTP |
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-Related structure data
Related structure data | 2zt5C 2zt6C 2zt7C 2zt8C 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: 78704.828 Da / Num. of mol.: 1 / Fragment: UNP residues 55-739 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GARS / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41250, glycine-tRNA ligase |
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#2: Chemical | ChemComp-B4P / |
#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: 3.5 Å3/Da / Density % sol: 64.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25mM Tris-HCL, 150mM NaCl, 10mM MgCl2, 4M Sodium formate, PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 15555 / Num. obs: 14819 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4 / Num. unique all: 1536 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PME Resolution: 3.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 174.9 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 1.3 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.52 Å
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