+Open data
-Basic information
Entry | Database: PDB / ID: 7sbn | |||||||||
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Title | Human glutaminase C (Y466W) with L-Gln, closed conformation | |||||||||
Components | Isoform 3 of Glutaminase kidney isoform, mitochondrial | |||||||||
Keywords | HYDROLASE / Cancer / Mitochondrial metabolism | |||||||||
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: 2.14 Å | |||||||||
Authors | Nguyen, T.-T.T. / Cerione, R.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: High-resolution structures of mitochondrial glutaminase C tetramers indicate conformational changes upon phosphate binding. Authors: Nguyen, T.T. / Ramachandran, S. / Hill, M.J. / Cerione, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sbn.cif.gz | 773.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sbn.ent.gz | 531.3 KB | Display | PDB format |
PDBx/mmJSON format | 7sbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/7sbn ftp://data.pdbj.org/pub/pdb/validation_reports/sb/7sbn | HTTPS FTP |
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-Related structure data
Related structure data | 7sbmC 5d3oS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59480.629 Da / Num. of mol.: 4 / Mutation: Y466W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / References: UniProt: O94925, glutaminase #2: Chemical | ChemComp-GLN / #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: 2.6 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 9% PEG 3350, 0.9 M LiCl and 0.1 M Tris pH 8.5 / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021 / Details: mirror focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→47.79 Å / Num. obs: 133802 / % possible obs: 98.46 % / Redundancy: 3 % / Biso Wilson estimate: 30.92 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.083 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.14→2.18 Å / Redundancy: 2.8 % / Num. unique obs: 12085 / CC1/2: 0.46 / CC star: 0.794 / Rpim(I) all: 0.482 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5d3o Resolution: 2.14→47.79 Å / SU ML: 0.2672 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9508 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: 40.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→47.79 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: 17.0913128506 Å / Origin y: 16.5730150906 Å / Origin z: 44.0358700838 Å
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Refinement TLS group | Selection details: all |