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Yorodumi- PDB-7ren: Room temperature serial crystal structure of Glutaminase C in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ren | ||||||
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Title | Room temperature serial crystal structure of Glutaminase C in complex with inhibitor UPGL-00004 | ||||||
Components | Glutaminase kidney isoform, mitochondrial | ||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Milano, S.K. / Finke, A. / Cerione, R.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: New insights into the molecular mechanisms of glutaminase C inhibitors in cancer cells using serial room temperature crystallography. Authors: Milano, S.K. / Huang, Q. / Nguyen, T.T. / Ramachandran, S. / Finke, A. / Kriksunov, I. / Schuller, D.J. / Szebenyi, D.M. / Arenholz, E. / McDermott, L.A. / Sukumar, N. / Cerione, R.A. / Katt, W.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ren.cif.gz | 724 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ren.ent.gz | 534.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ren.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/7ren ftp://data.pdbj.org/pub/pdb/validation_reports/re/7ren | HTTPS FTP |
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-Related structure data
Related structure data | 7rggC 5wj6S S: Starting model for refinement 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: 59457.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Production host: Escherichia coli (E. coli) / References: UniProt: O94925, glutaminase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.74 Å3/Da / Density % sol: 55.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.0 M lithium chloride, 10% PEG6000, 0.1 M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: G3 / Wavelength: 1.127 Å |
Detector | Type: DECTRIS EIGER2 X 1M / Detector: PIXEL / Date: Jun 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20.44 Å / Num. obs: 61831 / % possible obs: 97.9 % / Redundancy: 27.4 % / Biso Wilson estimate: 74.27 Å2 / CC1/2: 0.972 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.8→2.87 Å / Num. unique obs: 6026 / CC1/2: 0.12 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5WJ6 Resolution: 2.8→20.44 Å / SU ML: 0.4644 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.7766 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: 86.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.70250693539 Å / Origin y: 33.8976684625 Å / Origin z: -44.6124162783 Å
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Refinement TLS group | Selection details: all |