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- PDB-1nr1: Crystal structure of the R463A mutant of human Glutamate dehydrogenase -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nr1 | ||||||
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Title | Crystal structure of the R463A mutant of human Glutamate dehydrogenase | ||||||
![]() | Glutamate dehydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / glutamate dehydrogenase / hexamer / regulation | ||||||
Function / homology | ![]() L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamate catabolic process / glutamine metabolic process ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamate catabolic process / glutamine metabolic process / NAD+ binding / Mitochondrial protein degradation / substantia nigra development / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / ADP binding / mitochondrial matrix / GTP binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Banerjee, S. / Schmidt, T. / Fang, J. / Stanley, C.A. / Smith, T.J. | ||||||
![]() | ![]() Title: Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation Authors: Banerjee, S. / Schmidt, T. / Fang, J. / Stanley, C.A. / Smith, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 558.3 KB | Display | ![]() |
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PDB format | ![]() | 465 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55025.496 Da / Num. of mol.: 6 / Mutation: R463A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00367, glutamate dehydrogenase [NAD(P)+] |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: sodium phosphate, PEG 8000, BOG, sodium chloride, MPD, sodium azide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 55963 / Num. obs: 50903 / % possible obs: 91 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.3→3.45 Å / % possible all: 63 |
Reflection | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 20 Å / % possible obs: 64.6 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.032 |
Reflection shell | *PLUS % possible obs: 62.9 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6123 Å2 / ksol: 0.260803 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.53 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.226 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / Rfactor Rwork: 0.283 |