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Yorodumi- PDB-5a1n: The crystal structure of the GST-like domains complex of EPRS-AIM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a1n | ||||||
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Title | The crystal structure of the GST-like domains complex of EPRS-AIMP2 mutant S156D | ||||||
Components |
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Keywords | LIGASE / AIMP2 / EPRS / GST-LIKE DOMAIN | ||||||
Function / homology | Function and homology information type II pneumocyte differentiation / regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol ...type II pneumocyte differentiation / regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / positive regulation of protein ubiquitination / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / GTPase binding / protein-containing complex assembly / molecular adaptor activity / negative regulation of translation / protein ubiquitination / ribonucleoprotein complex / translation / negative regulation of cell population proliferation / apoptotic process / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cho, H.Y. / Choi, Y.S. / Kang, B.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Symmetric Assembly of a Decameric Subcomplex in Human Multi-tRNA Synthetase Complex Via Interactions between Glutathione Transferase-Homology Domains and Aspartyl-tRNA Synthetase. Authors: Cho, H.Y. / Lee, H.J. / Choi, Y.S. / Kim, D.K. / Jin, K.S. / Kim, S. / Kang, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a1n.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a1n.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 5a1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a1n_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
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Full document | 5a1n_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 5a1n_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 5a1n_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/5a1n ftp://data.pdbj.org/pub/pdb/validation_reports/a1/5a1n | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19310.699 Da / Num. of mol.: 1 / Fragment: GST-LIKE DOMAIN, RESIDUES 1-175 / Mutation: YES Source method: isolated from a genetically manipulated source Details: M1 TO R175 OF EPRS GST-LIKE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P07814, proline-tRNA ligase, glutamate-tRNA ligase | ||
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#2: Protein | Mass: 26818.926 Da / Num. of mol.: 1 / Fragment: GST-LIKE DOMAIN, RESIDUES 90-320 / Mutation: YES Source method: isolated from a genetically manipulated source Details: T90 TO K320 OF AIMP2 GST-LIKE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13155 | ||
#3: Chemical | #4: 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: 2.73 Å3/Da / Density % sol: 55.01 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 17% PEG 3350, 0.1M BIS-TRIS PH 5.5, 2MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 30430 / % possible obs: 99.3 % / Observed criterion σ(I): -2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 41 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.8 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TO BE PUBLISHED Resolution: 2.1→46.323 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.56 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.323 Å
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Refine LS restraints |
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LS refinement shell |
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