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- PDB-8grd: Crystal structure of a constitutively active mutant of the alpha ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8grd | ||||||
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Title | Crystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ADP and Mg | ||||||
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![]() | OXIDOREDUCTASE / Isocitrate dehydrogenase / NAD-dependent IDH / assembly / allosteric regulation | ||||||
Function / homology | ![]() : / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix ...: / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, X. / Sun, P. / Ding, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction. Authors: Chen, X. / Sun, P. / Liu, Y. / Shen, S. / Ma, T. / Ding, 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 | ![]() | 141.8 KB | Display | ![]() |
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PDB format | ![]() | 107.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 754.5 KB | Display | ![]() |
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Full document | ![]() | 758.8 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8grbC ![]() 8grgC ![]() 8grhC ![]() 8gruC ![]() 8gs5C ![]() 6kdfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 36625.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P50213, isocitrate dehydrogenase (NAD+) |
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#2: Protein | Mass: 39152.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.1 M sodium cacodylate (pH 5.1), 0.1 M calcium acetate, 10% (w/v) PEG 8000, 4 mM ADP, 4 mM CIT and 0.4 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.699→50 Å / Num. obs: 25101 / % possible obs: 100 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.029 / Rrim(I) all: 0.152 / Χ2: 0.478 / Net I/σ(I): 3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KDF Resolution: 2.699→23.313 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
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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 max: 119.4 Å2 / Biso mean: 50.1481 Å2 / Biso min: 25.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.699→23.313 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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