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- PDB-6aj8: Crystal structure of Trypanosoma brucei glycosomal isocitrate deh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aj8 | ||||||
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Title | Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+, alpha-ketoglutarate and ca2+ | ||||||
![]() | Isocitrate dehydrogenase [NADP] | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma brucei / glycosome / metabolism / isocitrate dehydrogenase | ||||||
Function / homology | ![]() isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / glycosome / tricarboxylic acid cycle / NAD binding / magnesium ion binding / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. ...Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K. | ||||||
![]() | ![]() Title: Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+) Authors: Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 352.9 KB | Display | ![]() |
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PDB format | ![]() | 291.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6aj6SC ![]() 6ajaC ![]() 6ajbC ![]() 6ajcC S: Starting model for refinement C: citing same article ( |
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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: 46791.590 Da / Num. of mol.: 2 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q387G0, isocitrate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AKG / | #5: Water | ChemComp-HOH / | Sequence details | The sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference ...The sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference available at uniprot at the time of data processing was derived from a different strain TRYPANOSOM | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG 1500, 100mM PCB buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 34871 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3339 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6AJ6 Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 22.856 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.798 / ESU R Free: 0.32 / 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: 51.845 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→20 Å
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Refine LS restraints |
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