+Open data
-Basic information
Entry | Database: PDB / ID: 6g2u | ||||||
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Title | Crystal structure of the human glutamate dehydrogenase 2 (hGDH2) | ||||||
Components | Glutamate dehydrogenase 2, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / glutamate / dehydrogenase | ||||||
Function / homology | Function and homology information L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / : / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamate catabolic process / Transcriptional activation of mitochondrial biogenesis ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / : / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamate catabolic process / Transcriptional activation of mitochondrial biogenesis / ADP binding / mitochondrial matrix / GTP binding / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93428699014 Å | ||||||
Authors | Fadouloglou, V.F. / Dimovasili, C. / Providaki, M. / Kotsifaki, D. / Sarrou, I. / Plaitakis, A. / Zaganas, I. / Kokkinidis, M. | ||||||
Funding support | Greece, 1items
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Citation | Journal: J.Neurochem. / Year: 2021 Title: Crystal structure of glutamate dehydrogenase 2, a positively selected novel human enzyme involved in brain biology and cancer pathophysiology. Authors: Dimovasili, C. / Fadouloglou, V.E. / Kefala, A. / Providaki, M. / Kotsifaki, D. / Kanavouras, K. / Sarrou, I. / Plaitakis, A. / Zaganas, I. / Kokkinidis, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g2u.cif.gz | 721.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g2u.ent.gz | 490.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/6g2u ftp://data.pdbj.org/pub/pdb/validation_reports/g2/6g2u | HTTPS FTP |
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-Related structure data
Related structure data | 1l1fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 56129.641 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Our construct lacks the 53 N-terminal residues which correspond to a leader peptide Source: (gene. exp.) Homo sapiens (human) / Gene: GLUD2, GLUDP1 / Cell line (production host): Sf21 / Production host: unidentified baculovirus References: UniProt: P49448, glutamate dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / #5: 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: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, MPD, NaCl, sodium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→48.15 Å / Num. obs: 83838 / % possible obs: 98.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 55.5027904224 Å2 / Rrim(I) all: 0.214 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.93→3.09 Å / Redundancy: 12.7 % / Num. unique obs: 11344 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L1F Resolution: 2.93428699014→47.6510455293 Å / SU ML: 0.403303580834 / Cross valid method: FREE R-VALUE / σ(F): 1.89429104804 / Phase error: 25.7425355641 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: 52.3493357802 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93428699014→47.6510455293 Å
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Refine LS restraints |
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LS refinement shell |
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