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- PDB-1ai2: ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ai2 | |||||||||
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Title | ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM (FLASH-COOLED) | |||||||||
![]() | ISOCITRATE DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / NADP / PHOSPHORYLATION / GLYOXYLATE BYPASS | |||||||||
Function / homology | ![]() isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / tricarboxylic acid cycle / electron transport chain / NAD binding / response to oxidative stress / magnesium ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stoddard, B.L. / Mesecar, A. / Koshland Junior, D.E. | |||||||||
![]() | ![]() Title: Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Authors: Mesecar, A.D. / Stoddard, B.L. / Koshland Jr., D.E. #1: ![]() Title: Determinants of Cofactor Specificity in Isocitrate Dehydrogenase: Structure of an Engineered Nadp+--> Nad+ Specificity-Reversal Mutant Authors: Hurley, J.H. / Chen, R. / Dean, A.M. #2: ![]() Title: Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Dinucleotide Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex Authors: Stoddard, B.L. / Dean, A. / Koshland Junior, D.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 77.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ai3C ![]() 1isoS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45809.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-ICA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.37 % Description: RESIDUES MUTATED IN 1ISO CHANGED BACK TO WILD TYPE SEQUENCE | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / Method: unknownDetails: Hurley, J.H., (1989) Proc. Natl. Acad. Sci. U.S.A., 86, 8635. | ||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 63007 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.14 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 183903 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ISO Resolution: 1.9→50 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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