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Yorodumi- PDB-5bmu: The crystal structure of the GST-like domains complex of AIMP3-EP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bmu | ||||||
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Title | The crystal structure of the GST-like domains complex of AIMP3-EPRS mutant C92SC105SC123S | ||||||
Components |
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Keywords | TRANSLATION/LIGASE / AIMP3 / EPRS / GST-like domain / TRANSLATION-LIGASE complex | ||||||
Function / homology | Function and homology information regulation of long-chain fatty acid import into cell / positive regulation of DNA damage response, signal transduction by p53 class mediator / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation ...regulation of long-chain fatty acid import into cell / positive regulation of DNA damage response, signal transduction by p53 class mediator / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / RNA stem-loop binding / GAIT complex / positive regulation of apoptotic signaling pathway / cellular response to leukemia inhibitory factor / cellular response to type II interferon / cellular response to insulin stimulus / positive regulation of cellular senescence / GTPase binding / negative regulation of translation / ribonucleoprotein complex / translation / positive regulation of apoptotic process / negative regulation of cell population proliferation / nucleolus / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Cho, H.J. / Kang, B.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Assembly of Multi-tRNA Synthetase Complex via Heterotetrameric Glutathione Transferase-homology Domains Authors: Cho, H.Y. / Maeng, S.J. / Cho, H.J. / Choi, Y.S. / Chung, J.M. / Lee, S. / Kim, H.K. / Kim, J.H. / Eom, C.Y. / Kim, Y.G. / Guo, M. / Jung, H.S. / Kang, B.S. / Kim, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bmu.cif.gz | 260.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bmu.ent.gz | 211.4 KB | Display | PDB format |
PDBx/mmJSON format | 5bmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/5bmu ftp://data.pdbj.org/pub/pdb/validation_reports/bm/5bmu | HTTPS FTP |
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-Related structure data
Related structure data | 4bvxSC 5a34C 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19428.141 Da / Num. of mol.: 4 / Fragment: UNP residues 1-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1E1, AIMP3, P18 / Production host: Escherichia coli (E. coli) / References: UniProt: O43324 #2: Protein | Mass: 19310.699 Da / Num. of mol.: 4 / Fragment: EPRS GST-like domain, UNP residues 1-175 / Mutation: C92S C105S C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS / Production host: Escherichia coli (E. coli) / References: UniProt: P07814, glutamate-tRNA ligase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: Ammonium sulfate, Sodium chloride, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 53953 / % possible obs: 100 % / Observed criterion σ(I): -2 / Redundancy: 5.4 % / Rsym value: 0.157 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BVX Resolution: 2.6→48.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.867 / SU B: 2.679 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.043 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.298 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→48.93 Å
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