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- PDB-6ajc: Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ajc | ||||||
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Title | Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate and ca2+ | ||||||
![]() | Isocitrate dehydrogenase [NADP] | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma cruzi / metabolism / isocitrate dehydrogenase | ||||||
Function / homology | ![]() isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / tricarboxylic acid cycle / NAD binding / magnesium ion binding 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 | ![]() | 646.2 KB | Display | ![]() |
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PDB format | ![]() | 538.5 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 ![]() 6aj8C ![]() 6ajaC ![]() 6ajbC 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: 46881.633 Da / Num. of mol.: 8 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CL Brener / Gene: Tc00.1047053506925.319 / Plasmid: pET-SUMO / Production host: ![]() ![]() References: UniProt: Q4E4L7, isocitrate dehydrogenase (NADP+) #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ICT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 8000, 100mM imidazole/HCl pH6.5, 3% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 14, 2017 |
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: 126184 / % possible obs: 86.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.02 / % possible all: 88.5 |
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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: 0.929 / Cor.coef. Fo:Fc free: 0.861 / SU B: 11.252 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / 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: 39.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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