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Yorodumi- PDB-7evt: Crystal structure of the N-terminal degron-truncated human glutam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7evt | ||||||
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Title | Crystal structure of the N-terminal degron-truncated human glutamine synthetase | ||||||
Components | Glutamine synthetase | ||||||
Keywords | LIGASE / Decamer / N-terminal truncated / N-degron | ||||||
Function / homology | Function and homology information protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity ...protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / Glutamate and glutamine metabolism / glutamate catabolic process / glial cell projection / response to glucose / cellular response to starvation / ribosome biogenesis / cell body / angiogenesis / cell population proliferation / endoplasmic reticulum / mitochondrion / extracellular exosome / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Chek, M.F. / Kim, S.Y. / Mori, T. / Hakoshima, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Crystal structure of N-terminal degron-truncated human glutamine synthetase. Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Kojima, H. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7evt.cif.gz | 740.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7evt.ent.gz | 520.7 KB | Display | PDB format |
PDBx/mmJSON format | 7evt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7evt_validation.pdf.gz | 533.9 KB | Display | wwPDB validaton report |
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Full document | 7evt_full_validation.pdf.gz | 578.7 KB | Display | |
Data in XML | 7evt_validation.xml.gz | 111.4 KB | Display | |
Data in CIF | 7evt_validation.cif.gz | 149.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/7evt ftp://data.pdbj.org/pub/pdb/validation_reports/ev/7evt | HTTPS FTP |
-Related structure data
Related structure data | 2qc8S 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
#1: Protein | Mass: 41856.023 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLUL, GLNS / Production host: Escherichia coli (E. coli) References: UniProt: P15104, glutamine synthetase, protein S-acyltransferase |
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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: 2.79 Å3/Da / Density % sol: 55.92 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.07 M sodium citrate (pH 5.1), 10% glycerol and 5.6% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 91909 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 83.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.24 |
Reflection shell | Resolution: 2.95→3.13 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 14650 / CC1/2: 0.882 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QC8 Resolution: 2.95→44.43 Å / SU ML: 0.3624 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7783 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→44.43 Å
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Refine LS restraints |
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LS refinement shell |
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