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Yorodumi- PDB-6dhl: Bovine glutamate dehydrogenase complexed with epicatechin-3-galla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dhl | |||||||||
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Title | Bovine glutamate dehydrogenase complexed with epicatechin-3-gallate (ECG) | |||||||||
Components | Glutamate dehydrogenase 1, mitochondrial | |||||||||
Keywords | OXIDOREDUCTASE / ECG / glutamate / dehydrogenase / inhibition | |||||||||
Function / homology | Function and homology information Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation ...Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial inner membrane / mitochondrial matrix / nucleotide binding / GTP binding / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.624 Å | |||||||||
Authors | Smith, T.J. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2011 Title: Green tea polyphenols control dysregulated glutamate dehydrogenase in transgenic mice by hijacking the ADP activation site. Authors: Li, C. / Li, M. / Chen, P. / Narayan, S. / Matschinsky, F.M. / Bennett, M.J. / Stanley, C.A. / Smith, T.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dhl.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6dhl.ent.gz | 961.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dhl_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 6dhl_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 6dhl_validation.xml.gz | 225.7 KB | Display | |
Data in CIF | 6dhl_validation.cif.gz | 285.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhl ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55127.648 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: A0A140T871, UniProt: P00366*PLUS, glutamate dehydrogenase #2: Chemical | ChemComp-XEG / ( |
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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: 52.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 5 mg/mL GDH in 0.4 mM ECG, 3 mM NADPH, 20 mM glutamate, 2:1 with reservoir solution (0.9 M sodium chloride, 50 mM TEA-HCl, 5 mM reduced glutathione, 8~9% PEG8000, 1 M 1,6-hexanediol), VAPOR ...Details: 5 mg/mL GDH in 0.4 mM ECG, 3 mM NADPH, 20 mM glutamate, 2:1 with reservoir solution (0.9 M sodium chloride, 50 mM TEA-HCl, 5 mM reduced glutathione, 8~9% PEG8000, 1 M 1,6-hexanediol), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2009 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 72322 / % possible obs: 95.01 % / Redundancy: 3 % / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 3.6→3.73 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.624→49.706 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.624→49.706 Å
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Refine LS restraints |
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LS refinement shell |
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