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Yorodumi- PDB-9c9q: Crystal structure of Chaetomium thermophilum Gcn2 HisRS-like domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c9q | ||||||
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Title | Crystal structure of Chaetomium thermophilum Gcn2 HisRS-like domain | ||||||
Components | non-specific serine/threonine protein kinase | ||||||
Keywords | TRANSFERASE / GCN2 Integrative stress response | ||||||
Function / homology | Function and homology information eukaryotic translation initiation factor 2alpha kinase activity / DNA damage checkpoint signaling / non-specific serine/threonine protein kinase / ATP binding Similarity search - Function | ||||||
Biological species | Thermochaetoides thermophila (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bou-Nader, C. / Bahmanjah, S. / Zhang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response Authors: Bou-Nader, C. / Gaikwad, S. / Bahmanjah, S. / Zhang, F. / Hinnebusch, A.G. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c9q.cif.gz | 245.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c9q.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 9c9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/9c9q ftp://data.pdbj.org/pub/pdb/validation_reports/c9/9c9q | HTTPS FTP |
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-Related structure data
Related structure data | 9c9rC 9cbsC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54232.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0028700 / Production host: Escherichia (bacteria) / Strain (production host): Arctic References: UniProt: G0S7T0, non-specific serine/threonine protein kinase #2: 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: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 100 mM sodium cacodylate pH 6.5, 30% w/v polyethylene glycol (PEG) 8000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.53 Å / Num. obs: 68536 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.37 Å2 / CC1/2: 0.993 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2→2.06 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 3881 / CC1/2: 0.286 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.53 Å / SU ML: 0.2578 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.3403 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→35.53 Å
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Refine LS restraints |
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LS refinement shell |
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