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Yorodumi- PDB-5z5e: Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z5e | ||||||
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Title | Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoarchaeum equitans | ||||||
Components | NEQ417 | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Nanoarchaeum equitans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å | ||||||
Authors | Noguchi, H. / Park, S.Y. / Tamura, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation. Authors: Fujisawa, A. / Toki, R. / Miyake, H. / Shoji, T. / Doi, H. / Hayashi, H. / Hanabusa, R. / Mutsuro-Aoki, H. / Umehara, T. / Ando, T. / Noguchi, H. / Voet, A. / Park, S.Y. / Tamura, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z5e.cif.gz | 210.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z5e.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 5z5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z5e ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z5e | HTTPS FTP |
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-Related structure data
Related structure data | 1atiS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 62897.102 Da / Num. of mol.: 2 / Fragment: UNP residues 2-512 / Mutation: L3P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea) Strain: Kin4-M / Gene: NEQ417 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74N31 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.76 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.05M sodium acetate trihydrate (pH 4.6), 1M ammonium sulfate and 3mg/ml protein |
-Data collection
Diffraction | Mean temperature: 93.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→50 Å / Num. obs: 70618 / % possible obs: 95.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.098→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.323 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ATI Resolution: 2.098→48.198 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.098→48.198 Å
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Refine LS restraints |
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LS refinement shell |
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