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- PDB-5h3f: Crystal structure of mouse isocitrate dehydrogenases 2 complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h3f | ||||||
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Title | Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate | ||||||
![]() | Isocitrate dehydrogenase [NADP], mitochondrial | ||||||
![]() | OXIDOREDUCTASE / NADP dependent isocitrate dehydrogenases 2 | ||||||
Function / homology | ![]() negative regulation of glial cell migration / Transcriptional activation of mitochondrial biogenesis / negative regulation of matrix metallopeptidase secretion / Citric acid cycle (TCA cycle) / NADP biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...negative regulation of glial cell migration / Transcriptional activation of mitochondrial biogenesis / negative regulation of matrix metallopeptidase secretion / Citric acid cycle (TCA cycle) / NADP biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / negative regulation of glial cell proliferation / tricarboxylic acid cycle / peroxisome / NAD binding / mitochondrial inner membrane / magnesium ion binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, Y. / Liu, L. / Miyakawa, T. / Nakamura, A. / Tanokura, M. | ||||||
![]() | ![]() Title: Studies on the regulatory mechanism of isocitrate dehydrogenase 2 using acetylation mimics Authors: Xu, Y. / Liu, L. / Nakamura, A. / Someya, S. / Miyakawa, T. / Tanokura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.6 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h3eC ![]() 1lwdS C: citing same article ( S: Starting model for refinement |
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Similar 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: 47891.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P54071, isocitrate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.14 Å3/Da / Density % sol: 79.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium tribasic dehydrate, 11.5%(v/v) 2-propanol, 10.8%(w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2014 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→45.9 Å / Num. obs: 35964 / % possible obs: 99.3 % / Redundancy: 10.4 % / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3.29→3.49 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.1 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LWD Resolution: 3.29→19.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 20.298 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.61 / ESU R Free: 0.33 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.8 Å2
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Refinement step | Cycle: LAST / Resolution: 3.29→19.89 Å
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Refine LS restraints |
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